Browse code

finally is all donw for Bioconductor

Emanuel Soda authored on 06/06/2022 09:35:54
Showing73 changed files

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 Package: ScreenR
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 Type: Package
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 Title: Package to Perform High Throughput Biological Screening
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-Version: 0.99.52
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+Version: 0.99.53
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 Date: 2022-04-01 
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 Authors@R: c(person("Emanuel Michele", "Soda", role = c("aut", "cre"),
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                   email = "emanuelsoda@gmail.com", 
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                   comment = c(ORICD = "0000-0002-2301-6465")),
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-             person("Elena", "Ceccacci", role = c("aut"),
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+            person("Elena", "Ceccacci", role = c("aut"),
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                    email = "elena.ceccacci@ieo.it", 
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-                   comment = c(ORICD = "0000-0002-2285-8994")))
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+                   comment = c(ORICD = "0000-0002-2285-8994")),
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+            person("Saverio", "Minucci", role = c("fnd", "ths"),
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+                   email = "saverio.minucci@ieo.it", 
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+                   comment = c(ORICD = "0000-0001-5678-536X")))
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 Description: ScreenR is a package suitable to perform hit identification in loss 
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             of function High Throughput Biological Screenings performed using 
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             barcoded shRNA-based  libraries. ScreenR combines the computing 
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@@ -18,7 +21,7 @@ Description: ScreenR is a package suitable to perform hit identification in loss
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             visualization modes for each step of the analysis.
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 License: MIT + file LICENSE
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 Encoding: UTF-8
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-RoxygenNote: 7.1.2
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+RoxygenNote: 7.2.0
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 Imports:
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     methods (>= 4.0),
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     rlang (>= 0.4),
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@@ -1,4 +1,10 @@
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-# ScreenR 0.99.52
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+# ScreenR 0.99.53
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+* Changes in version 0.99.53:
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+ * Update to the documentation for the example dataset as requested by the 
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+   reviewer
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+ * Pushed to Bioconductor
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+
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+
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 * Changes in version 0.99.52:
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  * Pushed to Bioconductor
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@@ -5,52 +5,81 @@
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 #' @concept  data
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 #'
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 #' @format A data frame with 5323 rows and 15 variables obtained from
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-#'         barcode alignment to the reference genome/library.
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+#'         barcode alignment to the reference library.
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+#'         It is generated from a [Cellecta](https://cellecta.com/) protocol.
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+#'         The samples generated are then sequenced using an RNA-seq protocol.
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+#'         Due to the fact that different shRNAs are sequenced for a gene each
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+#'         barcode has its associated reads. This reads were aligned to the
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+#'         reference library using [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
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+#'         and then sorted with [samtools](https://github.com/samtools/samtools).
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+#'         Since this dataset comes from a Chemical Synthetic Lethality
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+#'         experiments the samples treated and combined with the shRNAs
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+#'         knockdown should present a decreased number of reads compared to
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+#'         the controls.
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+#'
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 #' \describe{
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 #'   \item{Barcode}{It contains an ID that identify each barcode. It can be use
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 #'   to marge the annotation table with the count table. A Barcode is a unique
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 #'   identifier of an shRNA. In a genetic screening multiple slightly different
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-#'   shRNAs perform a knockout a gene each with its efficacy. For this reason
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-#'   it is importat to keep track of each shRNA using a unique barcode.}
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+#'   shRNAs perform a knockout of a gene each with its efficacy. For this reason
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+#'   it is important to keep track of each shRNA using a unique barcode.}
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+#'
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+#'  \item{Time_1}{It contains the counts at time zero.
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+#'                This is the first time point at which cells are not treated
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+#'                and not infected.}
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 #'
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-#'  \item{Time_1}{It contains the counts at time zero}
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+#'   \item{Time_2}{It contains the counts after the cell were washed.
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+#'                At this time point the cells are  infected and following the
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+#'                Cellecta protocol are washed with the puromycin.}
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 #'
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-#'   \item{Time_2}{It contains the counts after the cell were washed}
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 #'   \item{Time_3_TRT_rep1}{It contains the counts for the first replicate
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-#'                 of the treated at the first time point}
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+#'                 of the treated at the first time point.
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+#'                 Usually the first time  point is 7 day after the puromycin
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+#'                 wash.}
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 #'
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 #'   \item{Time_3_TRT_rep2}{It contains the counts for the second replicate
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-#'                 of the treated at the first time point}
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+#'                 of the treated at the first time point. Usually the first
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+#'                 time point is 7 day after the puromycin wash.}
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 #'
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 #'   \item{Time_3_TRT_rep3}{It contains the counts for the third replicate
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-#'                 of the treated at the first time point}
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+#'                 of the treated at the first time point. Usually the first
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+#'                 time point is 7 day after the puromycin wash.}
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 #'
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 #'   \item{Time_3_rep1}{It contains the counts for the first replicate of the
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-#'                 control at the first time point}
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+#'                 control at the first time point. Usually the first
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+#'                 time point is 7 day after the puromycin wash.}
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 #'
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 #'   \item{Time_3_rep2}{It contains the counts for the second replicate of the
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-#'                 control at the first time point}
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+#'                 control at the first time point. Usually the first
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+#'                 time point is 7 day after the puromycin wash.}
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 #'
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 #'   \item{Time_3_rep3}{It contains the counts for the third replicate of the
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-#'                 control at the first time point}
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+#'                 control at the first time point. Usually the first
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+#'                 time point is 7 day after the puromycin  wash.}
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 #'
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 #'   \item{Time_4_TRT_rep1}{It contains the counts for the first replicate
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-#'                 of the treated at the second time point}
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+#'                 of the treated at the second time point. Usually the first
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+#'                 time point is 14 day after the puromycin wash.}
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 #'
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 #'   \item{Time_4_TRT_rep2}{It contains the counts for the second replicate
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-#'                 of the treated at the second time point}
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+#'                 of the treated at the second time point. Usually the first
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+#'                 time point is 14 day after the puromycin wash.}
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 #'
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 #'   \item{Time_4_TRT_rep3}{It contains the counts for the third replicate
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-#'                 of the treated at the second time point}
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+#'                 of the treated at the second time point. Usually the first
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+#'                 time point is 14 day after the puromycin wash.}
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 #'
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 #'   \item{Time_4_rep1}{It contains the counts for the first replicate of the
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-#'                 control at the second time point}
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+#'                 control at the second time point. Usually the first
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+#'                 time point is 14 day after the puromycin wash.}
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 #'
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 #'   \item{Time_4_rep2}{It contains the counts for the second replicate of the
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-#'                 control at the second time point}
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+#'                 control at the second time point. Usually the first
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+#'                 time point is 14 day after the puromycin wash.}
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 #'
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 #'   \item{Time_4_rep3}{It contains the counts for the third replicate of the
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-#'                 control at the second time point}
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+#'                 control at the second time point. Usually the first
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+#'                 time point is 14 day after the puromycin wash.}
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 #' }
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 #'
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 "count_table"
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 #' obj
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 create_screenr_object <- function(table = NULL, annotation = NULL,
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                                   groups = NULL, replicates = c("")) {
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-    # arcode <- as.factor(table$Barcode)
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-    annotation$Barcode <- as.factor(annotation$Barcode)
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     object <- methods::new("screenr_object",
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                            count_table = tibble(table),
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-                           annotation_table = tibble(annotation), groups = groups,
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-                           replicates = replicates, normalized_count_table = tibble(),
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+                           annotation_table = tibble(annotation),
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+                           groups = as.factor(groups),
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+                           replicates = replicates,
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+                           normalized_count_table = tibble(),
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                            data_table = tibble()
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     )
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     return(object)
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 #' )
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 screenr_object <- setClass("screenr_object", methods::representation(
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   count_table = "data.frame",
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-  annotation_table = "data.frame", groups = "factor", replicates = "vector",
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-  normalized_count_table = "data.frame", data_table = "data.frame"
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+  annotation_table = "data.frame",
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+  groups = "factor",
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+  replicates = "vector",
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+  normalized_count_table = "data.frame",
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+  data_table = "data.frame"
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 ))
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">ScreenR</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
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       </span>
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     </div>
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       <h1>License</h1>
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     </div>
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-<pre>YEAR: 2021
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+<pre>YEAR: 2022
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 COPYRIGHT HOLDER: ScreenR authors
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+
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 </pre>
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   </div>
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@@ -71,7 +72,7 @@ COPYRIGHT HOLDER: ScreenR authors
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       <footer><div class="copyright">
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
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 </div>
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 <div class="pkgdown">
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">ScreenR</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
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       </span>
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     </div>
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... ...
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 <div id="mit-license" class="section level1">
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-<p>Copyright (c) 2021 ScreenR authors</p>
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+<p>Copyright (c) 2022 ScreenR authors</p>
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 <p>Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:</p>
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 <p>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.</p>
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 <p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
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       <footer><div class="copyright">
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
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 </div>
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 <div class="pkgdown">
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ScreenR</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
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       </span>
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     </div>
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... ...
@@ -99,6 +99,7 @@ Ceccacci</h4>
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 Italy<br><a class="author_email" href="mailto:#"></a><a href="mailto:elena.ceccacci@ieo.it" class="email">elena.ceccacci@ieo.it</a>
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       </address>
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+            <h4 data-toc-skip class="date">2022-06-06</h4>
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       <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/vignettes/Analysis_Example.Rmd" class="external-link"><code>vignettes/Analysis_Example.Rmd</code></a></small>
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       <div class="hidden name"><code>Analysis_Example.Rmd</code></div>
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@@ -113,8 +114,17 @@ Italy<br><a class="author_email" href="mailto:#"></a><a href="mailto:elena.cecca
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 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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 <code class="sourceCode R"><span class="fu">knitr</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/knitr/man/opts_chunk.html" class="external-link">opts_chunk</a></span><span class="op">$</span><span class="fu">set</span><span class="op">(</span>collapse <span class="op">=</span> <span class="cn">TRUE</span>, comment <span class="op">=</span> <span class="st">"#&gt;"</span><span class="op">)</span>
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 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
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-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
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-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyr.tidyverse.org" class="external-link">tidyr</a></span><span class="op">)</span></code></pre></div>
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+<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
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+<pre><code><span class="co">## </span>
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+<span class="co">## Attaching package: 'dplyr'</span></code></pre>
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+<pre><code><span class="co">## The following objects are masked from 'package:stats':</span>
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+<span class="co">## </span>
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+<span class="co">##     filter, lag</span></code></pre>
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+<pre><code><span class="co">## The following objects are masked from 'package:base':</span>
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+<span class="co">## </span>
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+<span class="co">##     intersect, setdiff, setequal, union</span></code></pre>
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+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyr.tidyverse.org" class="external-link">tidyr</a></span><span class="op">)</span></code></pre></div>
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 </div>
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 <div class="section level2">
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 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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@@ -128,7 +138,7 @@ screening, has greatly increased for their benefits both from a
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 time-consuming point of view and for the possibility of carrying out
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 screening on a large number of genes simultaneously. However, the
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 bioinformatic analysis of this type of screening still lacks a golden
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-standard. Here, screenR allows the user to carry out a preliminary
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+standard. Here, ScreenR allows the user to carry out a preliminary
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 quality check of the experiment, visually inspect the data and finally
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 identify the most significant hits of the experiment through a series of
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 plots and cross-statistical analyses.</p>
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@@ -143,32 +153,21 @@ plots and cross-statistical analyses.</p>
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 packages to be installed. Dependencies are usually handled
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 automatically, when installing the package using the following
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 commands:</p>
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-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span>
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+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
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+<code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st">"BiocManager"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span>
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+    <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span>
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+
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 <span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span></code></pre></div>
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 </div>
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 <div class="section level3">
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-<h3 id="manual-installation">Manual installation<a class="anchor" aria-label="anchor" href="#manual-installation"></a>
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+<h3 id="github">Github<a class="anchor" aria-label="anchor" href="#github"></a>
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 </h3>
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-<p>In the unlikely case that a manual installation is required, e.g., if
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-you do not install <strong>ScreenR</strong> via Bioconductor (which is
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-highly recommended), you can install CRAN packages using:</p>
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-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"&lt;package_name&gt;"</span><span class="op">)</span></code></pre></div>
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-<p>While Bioconductor packages can be installed from R using the
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-following command:</p>
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-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"&lt;package_name&gt;"</span><span class="op">)</span></code></pre></div>
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-<p>Sometimes, it may also be useful to update Bioconductor:</p>
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-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
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-<p>Finally, the manual installation of <strong>ScreenR</strong> can, for
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-example, be done from the command line …</p>
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-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>R CMD INSTALL ScreenR_<span class="sc">&lt;</span>version<span class="sc">&gt;</span>.tar.gz</span></code></pre></div>
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-<p>… or the newest version can directly be installed from GitHub using
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-the CRAN package devtools:</p>
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+<p>The newest version can directly be installed from GitHub using the
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+CRAN package devtools:</p>
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 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="co"># install.packages("devtools")</span>
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+<code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://devtools.r-lib.org/" class="external-link">"devtools"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span>
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+   <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span>
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+
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 <span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"EmanuelSoda/ScreenR"</span><span class="op">)</span></code></pre></div>
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 </div>
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 </div>
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@@ -182,14 +181,23 @@ the CRAN package devtools:</p>
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 </h3>
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 <p>After installation, loading the package is simple as :</p>
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 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://emanuelsoda.github.io/ScreenR/" class="external-link">ScreenR</a></span><span class="op">)</span></code></pre></div>
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+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://emanuelsoda.github.io/ScreenR/" class="external-link">ScreenR</a></span><span class="op">)</span>
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+<span class="co">#&gt; </span>
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+<span class="co">#&gt; Welcome to ScreenR</span>
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+<span class="co">#&gt; --------------------------</span>
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+<span class="co">#&gt; </span>
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+<span class="co">#&gt; See ?ScreenR for a list of</span>
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+<span class="co">#&gt; available functions.</span>
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+<span class="co">#&gt; </span>
192
+<span class="co">#&gt; Enjoy!</span>
193
+<span class="co">#&gt; </span></code></pre></div>
186 194
 </div>
187 195
 <div class="section level3">
188 196
 <h3 id="read-data">Read Data<a class="anchor" aria-label="anchor" href="#read-data"></a>
189 197
 </h3>
190 198
 <p>The input of ScreenR is a count table obtained from barcode alignment
191 199
 to the reference genome/library. A count table is usually the starting
192
-point of an RNA-seq differentially expressed genes analysis and consists
200
+point of an RNA-seq deferentially expressed genes analysis and consists
193 201
 of a matrix containing reads count organized with:</p>
194 202
 <ul>
195 203
 <li>Genes on the rows</li>
... ...
@@ -198,8 +206,26 @@ of a matrix containing reads count organized with:</p>
198 206
 <p>For this vignette we will use as an example a Loss of Function
199 207
 Chemical lethality Genetic Screening performed using shRNA libraries
200 208
 where each gene is represented by ten slightly different shRNA each
201
-labeled with a univoce barcode. First of all the data has to be
202
-read.</p>
209
+labeled with a unique barcode coming from an unpublished dataset
210
+generated using the <a href="https://cellecta.com/" class="external-link">Cellecta</a>
211
+protocol.</p>
212
+<p>First of all the data has to be read. Then another very important
213
+step is to set up the column names in the following way:</p>
214
+<ul>
215
+<li>The first part of the string is the timepoint</li>
216
+<li>The second is the type of sample (example: treated or control or the
217
+name of the treatment)</li>
218
+<li>Third slot is a way to make each replicate unique (for example a
219
+letter or a number)</li>
220
+</ul>
221
+<p>In the end we have</p>
222
+<p><strong><code>Time point_Type of sample_replicate</code></strong></p>
223
+<p>and for example we could have <strong>h24_control_1</strong> which
224
+mean the first replicate of the control sample at 24 hour.</p>
225
+<p>Since this dataset comes from a Chemical Synthetic Lethality
226
+experiments the samples treated with the drug combined with the shRNAs
227
+knockdown should present a decreased number of reads compared to the
228
+controls.</p>
203 229
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
204 230
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">count_table</span><span class="op">)</span>
205 231
 <span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">annotation_table</span><span class="op">)</span>
... ...
@@ -211,9 +237,10 @@ read.</p>
211 237
     <span class="st">"Time4_TRT_A"</span>, <span class="st">"Time4_TRT_B"</span>, <span class="st">"Time4_TRT_C"</span>, 
212 238
     <span class="st">"Time4_CTRL_A"</span>, <span class="st">"Time4_CTRL_B"</span>, <span class="st">"Time4_CTRL_C"</span>
213 239
 <span class="op">)</span>
214
-<span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
215
-    <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Barcode <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">Barcode</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
216
-    <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Barcode</span> <span class="op">!=</span> <span class="st">"*"</span><span class="op">)</span>
240
+<span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://tidyr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
241
+    <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Barcode <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">Barcode</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://tidyr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
242
+    <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Barcode</span> <span class="op">!=</span> <span class="st">"*"</span><span class="op">)</span> <span class="op"><a href="https://tidyr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  
243
+  <span class="fu"><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span><span class="op">)</span>
217 244
 
218 245
 
219 246
 <span class="va">total_Annotation</span> <span class="op">&lt;-</span> <span class="va">annotation_table</span></code></pre></div>
... ...
@@ -263,7 +290,7 @@ mathematical expression:</p>
263 290
 reads \; to \; a \; barcode}
264 291
              { \sum_{sample}{Number\; of \;mapped \; reads}}
265 292
 *10^{6}\]</span></p>
266
-<p>The number of reads mapped for each Barcode in a sample are
293
+<p>The number of reads mapped for each barcode in a sample are
267 294
 normalized by the number of reads in that sample and multiplied by one
268 295
 million.</p>
269 296
 <p>This information is store in a <em>data table</em> which is a tidy
... ...
@@ -294,7 +321,8 @@ the formula.</p>
294 321
 <span class="va">plot</span></code></pre></div>
295 322
 <p><img src="Analysis_Example_files/figure-html/plot_mapped_reads-1.png" width="700"></p>
296 323
 <p>For example the distribution can be seen using both boxplots or
297
-density plots. #### Boxplot Mapped Reads</p>
324
+density plots.</p>
325
+<p>#### Boxplot Mapped Reads</p>
298 326
 <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
299 327
 <code class="sourceCode R"><span class="va">plot</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/plot_mapped_reads_distribution.html">plot_mapped_reads_distribution</a></span><span class="op">(</span>
300 328
     <span class="va">object</span>, <span class="va">palette</span>,
... ...
@@ -365,8 +393,8 @@ in the plot_mds function.</p>
365 393
 <h5 id="for-treatment">For Treatment<a class="anchor" aria-label="anchor" href="#for-treatment"></a>
366 394
 </h5>
367 395
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
368
-<code class="sourceCode R"><span class="va">group_table</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/get_data_table.html">get_data_table</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span>   <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
369
-    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Sample</span>, <span class="va">Day</span>, <span class="va">Treatment</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
396
+<code class="sourceCode R"><span class="va">group_table</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/get_data_table.html">get_data_table</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span>   <span class="op"><a href="https://tidyr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
397
+    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Sample</span>, <span class="va">Day</span>, <span class="va">Treatment</span><span class="op">)</span> <span class="op"><a href="https://tidyr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
370 398
     <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span>
371 399
 <span class="co">#&gt; ScreenR normalized data table containing:</span>
372 400
 <span class="co">#&gt;  74438 rows</span>
... ...
@@ -405,7 +433,8 @@ ScreenR is based on three different methods:</p>
405 433
 filtering</a></li>
406 434
 <li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458527/" class="external-link">CAMERA
407 435
 filtering</a></li>
408
-<li>[ROAST filtering]/<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922896/" class="external-link uri">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922896/</a>)</li>
436
+<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922896/" class="external-link">ROAST
437
+filtering</a></li>
409 438
 </ul>
410 439
 <div class="section level4">
411 440
 <h4 id="z-score-hit">Z-score hit<a class="anchor" aria-label="anchor" href="#z-score-hit"></a>
... ...
@@ -557,36 +586,36 @@ function<br><em>find_roast_hit</em>.</p>
557 586
 
558 587
 <span class="va">roast_hit_TRT</span>
559 588
 <span class="co">#&gt; $Time3</span>
560
-<span class="co">#&gt; <span style="color: #949494;"># A tibble: 30 × 9</span></span>
589
+<span class="co">#&gt; <span style="color: #949494;"># A tibble: 29 × 9</span></span>
561 590
 <span class="co">#&gt;    Gene   NGenes PropDown PropUp Direction PValue     FDR PValue.Mixed FDR.Mixed</span>
562 591
 <span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
563 592
 <span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gene_…     12    0.917    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.006<span style="text-decoration: underline;">68</span>       0.000<span style="text-decoration: underline;">1</span>    0.013<span style="text-decoration: underline;">4</span></span>
564 593
 <span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gene_…     12    0.833    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.006<span style="text-decoration: underline;">68</span>       0.000<span style="text-decoration: underline;">1</span>    0.013<span style="text-decoration: underline;">4</span></span>
565
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gene_…     10    0.7      0   Down      0.000<span style="text-decoration: underline;">1</span> 0.006<span style="text-decoration: underline;">68</span>       0.000<span style="text-decoration: underline;">7</span>    0.080<span style="text-decoration: underline;">1</span></span>
566
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gene_…     10    0.5      0.1 Down      0.000<span style="text-decoration: underline;">7</span> 0.056<span style="text-decoration: underline;">4</span>        0.002<span style="text-decoration: underline;">9</span>    0.152 </span>
567
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gene_…     10    0.3      0   Down      0.000<span style="text-decoration: underline;">7</span> 0.056<span style="text-decoration: underline;">4</span>        0.015<span style="text-decoration: underline;">9</span>    0.205 </span>
568
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gene_…     10    0.4      0   Down      0.000<span style="text-decoration: underline;">9</span> 0.056<span style="text-decoration: underline;">4</span>        0.019<span style="text-decoration: underline;">3</span>    0.222 </span>
569
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gene_…     10    0.5      0   Down      0.001<span style="text-decoration: underline;">2</span> 0.061<span style="text-decoration: underline;">4</span>        0.022<span style="text-decoration: underline;">3</span>    0.228 </span>
570
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gene_…     10    0.2      0   Down      0.006<span style="text-decoration: underline;">2</span> 0.205         0.075<span style="text-decoration: underline;">4</span>    0.406 </span>
571
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gene_…     10    0.4      0.1 Down      0.007<span style="text-decoration: underline;">2</span> 0.224         0.010<span style="text-decoration: underline;">3</span>    0.161 </span>
572
-<span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gene_…     10    0.2      0   Down      0.007<span style="text-decoration: underline;">6</span> 0.224         0.019<span style="text-decoration: underline;">4</span>    0.222 </span>
573
-<span class="co">#&gt; <span style="color: #949494;"># … with 20 more rows</span></span>
594
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gene_…     10    0.7      0   Down      0.000<span style="text-decoration: underline;">1</span> 0.006<span style="text-decoration: underline;">68</span>       0.000<span style="text-decoration: underline;">5</span>    0.060<span style="text-decoration: underline;">1</span></span>
595
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gene_…     10    0.4      0   Down      0.000<span style="text-decoration: underline;">2</span> 0.016<span style="text-decoration: underline;">0</span>        0.020<span style="text-decoration: underline;">2</span>    0.229 </span>
596
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gene_…     10    0.5      0.1 Down      0.000<span style="text-decoration: underline;">6</span> 0.048<span style="text-decoration: underline;">9</span>        0.001<span style="text-decoration: underline;">6</span>    0.109 </span>
597
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gene_…     10    0.3      0   Down      0.000<span style="text-decoration: underline;">7</span> 0.049<span style="text-decoration: underline;">6</span>        0.017     0.221 </span>
598
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gene_…     10    0.5      0   Down      0.001<span style="text-decoration: underline;">1</span> 0.068<span style="text-decoration: underline;">2</span>        0.024<span style="text-decoration: underline;">5</span>    0.261 </span>
599
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gene_…     10    0.2      0   Down      0.006<span style="text-decoration: underline;">1</span> 0.199         0.019<span style="text-decoration: underline;">4</span>    0.227 </span>
600
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gene_…     10    0.2      0   Down      0.006<span style="text-decoration: underline;">4</span> 0.199         0.078<span style="text-decoration: underline;">8</span>    0.415 </span>
601
+<span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gene_…     10    0.4      0.1 Down      0.008  0.236         0.009<span style="text-decoration: underline;">8</span>    0.155 </span>
602
+<span class="co">#&gt; <span style="color: #949494;"># … with 19 more rows</span></span>
574 603
 <span class="co">#&gt; </span>
575 604
 <span class="co">#&gt; $Time4</span>
576
-<span class="co">#&gt; <span style="color: #949494;"># A tibble: 104 × 9</span></span>
605
+<span class="co">#&gt; <span style="color: #949494;"># A tibble: 106 × 9</span></span>
577 606
 <span class="co">#&gt;    Gene   NGenes PropDown PropUp Direction PValue     FDR PValue.Mixed FDR.Mixed</span>
578 607
 <span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
579
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gene_…     12      1      0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
580
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gene_…     12      1      0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
581
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gene_…     10      0.9    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
582
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gene_…     10      0.9    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
583
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gene_…     10      0.7    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
584
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gene_…     10      0.7    0.1 Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
585
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gene_…     10      0.7    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">809</span></span>
586
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gene_…     10      0.6    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.001<span style="text-decoration: underline;">5</span>  0.005<span style="text-decoration: underline;">78</span> </span>
587
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gene_…     10      0.4    0.1 Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">2</span>  0.001<span style="text-decoration: underline;">74</span> </span>
588
-<span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gene_…     10      0.4    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.011<span style="text-decoration: underline;">7</span>  0.024<span style="text-decoration: underline;">7</span>  </span>
589
-<span class="co">#&gt; <span style="color: #949494;"># … with 94 more rows</span></span></code></pre></div>
608
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gene_…     12      1      0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
609
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gene_…     12      1      0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
610
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gene_…     10      0.9    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
611
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gene_…     10      0.7    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
612
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gene_…     10      0.7    0.1 Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
613
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gene_…     10      0.7    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
614
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gene_…     10      0.7    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">1</span>  0.000<span style="text-decoration: underline;">703</span></span>
615
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gene_…     10      0.6    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">3</span>  0.001<span style="text-decoration: underline;">99</span> </span>
616
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gene_…     10      0.4    0.1 Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.000<span style="text-decoration: underline;">3</span>  0.001<span style="text-decoration: underline;">99</span> </span>
617
+<span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gene_…     10      0.4    0   Down      0.000<span style="text-decoration: underline;">1</span> 0.002<span style="text-decoration: underline;">05</span>       0.014<span style="text-decoration: underline;">2</span>  0.028<span style="text-decoration: underline;">4</span>  </span>
618
+<span class="co">#&gt; <span style="color: #949494;"># … with 96 more rows</span></span></code></pre></div>
590 619
 </div>
591 620
 <div class="section level4">
592 621
 <h4 id="find-common-hit">Find Common Hit<a class="anchor" aria-label="anchor" href="#find-common-hit"></a>
... ...
@@ -649,11 +678,18 @@ function <strong>plot_trend</strong>.</p>
649 678
 <code class="sourceCode R"><span class="va">candidate_hits</span> <span class="op">&lt;-</span> <span class="va">common_hit_TRT_at_least_2</span><span class="op">$</span><span class="va">Time3</span>
650 679
 
651 680
 <span class="fu"><a href="../reference/plot_trend.html">plot_trend</a></span><span class="op">(</span>screenR_Object <span class="op">=</span> <span class="va">object</span>, 
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-           genes <span class="op">=</span> <span class="va">candidate_hits</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, 
681
+           genes <span class="op">=</span> <span class="va">candidate_hits</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, 
653 682
            nrow <span class="op">=</span> <span class="fl">2</span>, ncol <span class="op">=</span> <span class="fl">2</span>, 
654 683
            group_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Time1"</span>, <span class="st">"Time2"</span>, <span class="st">"TRT"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
655 684
 <p><img src="Analysis_Example_files/figure-html/plot_trend-1.png" width="700"></p>
656 685
 <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
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+<code class="sourceCode R">
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+<span class="fu"><a href="../reference/plot_trend.html">plot_trend</a></span><span class="op">(</span>screenR_Object <span class="op">=</span> <span class="va">object</span>, 
688
+           genes <span class="op">=</span> <span class="va">candidate_hits</span><span class="op">[</span><span class="fl">2</span><span class="op">]</span>, 
689
+           nrow <span class="op">=</span> <span class="fl">2</span>, ncol <span class="op">=</span> <span class="fl">2</span>, 
690
+           group_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Time1"</span>, <span class="st">"Time2"</span>, <span class="st">"TRT"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
691
+<p><img src="Analysis_Example_files/figure-html/plot_trend-2.png" width="700"></p>
692
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
657 693
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span>
658 694
 <span class="co">#&gt; R version 4.2.0 (2022-04-22)</span>
659 695
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... ...
@@ -670,7 +706,7 @@ function <strong>plot_trend</strong>.</p>
670 706
 <span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span>
671 707
 <span class="co">#&gt; </span>
672 708
 <span class="co">#&gt; other attached packages:</span>
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-<span class="co">#&gt; [1] ScreenR_0.99.5   tidyr_1.2.0      dplyr_1.0.9      ggplot2_3.3.6   </span>
709
+<span class="co">#&gt; [1] ScreenR_0.99.53  tidyr_1.2.0      dplyr_1.0.9      ggplot2_3.3.6   </span>
674 710
 <span class="co">#&gt; [5] BiocStyle_2.24.0</span>
675 711
 <span class="co">#&gt; </span>
676 712
 <span class="co">#&gt; loaded via a namespace (and not attached):</span>
... ...
@@ -682,19 +718,19 @@ function <strong>plot_trend</strong>.</p>
682 718
 <span class="co">#&gt; [16] rmarkdown_2.14      pkgdown_2.0.3       textshaping_0.3.6  </span>
683 719
 <span class="co">#&gt; [19] desc_1.4.1          labeling_0.4.2      splines_4.2.0      </span>
684 720
 <span class="co">#&gt; [22] stringr_1.4.0       munsell_0.5.0       compiler_4.2.0     </span>
685
-<span class="co">#&gt; [25] xfun_0.30           pkgconfig_2.0.3     systemfonts_1.0.4  </span>
721
+<span class="co">#&gt; [25] xfun_0.31           pkgconfig_2.0.3     systemfonts_1.0.4  </span>
686 722
 <span class="co">#&gt; [28] mgcv_1.8-40         htmltools_0.5.2     tidyselect_1.1.2   </span>
687 723
 <span class="co">#&gt; [31] tibble_3.1.7        ggvenn_0.1.9        bookdown_0.26      </span>
688
-<span class="co">#&gt; [34] edgeR_3.38.0        fansi_1.0.3         crayon_1.5.1       </span>
724
+<span class="co">#&gt; [34] edgeR_3.38.1        fansi_1.0.3         crayon_1.5.1       </span>
689 725
 <span class="co">#&gt; [37] withr_2.5.0         grid_4.2.0          nlme_3.1-157       </span>
690 726
 <span class="co">#&gt; [40] jsonlite_1.8.0      gtable_0.3.0        lifecycle_1.0.1    </span>
691 727
 <span class="co">#&gt; [43] DBI_1.1.2           magrittr_2.0.3      scales_1.2.0       </span>
692 728
 <span class="co">#&gt; [46] cli_3.3.0           stringi_1.7.6       cachem_1.0.6       </span>
693
-<span class="co">#&gt; [49] farver_2.1.0        fs_1.5.2            limma_3.52.0       </span>
729
+<span class="co">#&gt; [49] farver_2.1.0        fs_1.5.2            limma_3.52.1       </span>
694 730
 <span class="co">#&gt; [52] bslib_0.3.1         ellipsis_0.3.2      ragg_1.2.2         </span>
695 731
 <span class="co">#&gt; [55] generics_0.1.2      vctrs_0.4.1         tools_4.2.0        </span>
696 732
 <span class="co">#&gt; [58] glue_1.6.2          purrr_0.3.4         fastmap_1.1.0      </span>
697
-<span class="co">#&gt; [61] yaml_2.3.5          colorspace_2.0-3    BiocManager_1.30.17</span>
733
+<span class="co">#&gt; [61] yaml_2.3.5          colorspace_2.0-3    BiocManager_1.30.18</span>
698 734
 <span class="co">#&gt; [64] memoise_2.0.1       knitr_1.39          patchwork_1.1.1    </span>
699 735
 <span class="co">#&gt; [67] sass_0.4.1</span></code></pre></div>
700 736
 </div>
... ...
@@ -714,7 +750,7 @@ function <strong>plot_trend</strong>.</p>
714 750
 
715 751
       <footer><div class="copyright">
716 752
   <p></p>
717
-<p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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718 754
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17 17
       </button>
18 18
       <span class="navbar-brand">
19 19
         <a class="navbar-link" href="../index.html">ScreenR</a>
20
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
20
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
21 21
       </span>
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... ...
@@ -68,7 +68,7 @@
68 68
 
69 69
 
70 70
       <footer><div class="copyright">
71
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
72 72
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17 17
       </button>
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       <span class="navbar-brand">
19 19
         <a class="navbar-link" href="index.html">ScreenR</a>
20
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
20
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
21 21
       </span>
22 22
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23 23
 
... ...
@@ -66,6 +66,10 @@
66 66
           <p><strong>Elena Ceccacci</strong>. Author. 
67 67
           <br><small>0000-0002-2285-8994</small></p>
68 68
         </li>
69
+        <li>
70
+          <p><strong>Saverio Minucci</strong>. Funder, thesis advisor. 
71
+          <br><small>0000-0001-5678-536X</small></p>
72
+        </li>
69 73
       </ul></div>
70 74
     <div class="section level2 citation-section">
71 75
     <div>
... ...
@@ -77,13 +81,13 @@
77 81
 
78 82
     <p>Soda E, Ceccacci E (2022).
79 83
 <em>ScreenR: Package to Perform High Throughput Biological Screening</em>.
80
-R package version 0.99.5, <a href="https://emanuelsoda.github.io/ScreenR/" class="external-link">https://emanuelsoda.github.io/ScreenR/</a>. 
84
+R package version 0.99.53, <a href="https://emanuelsoda.github.io/ScreenR/" class="external-link">https://emanuelsoda.github.io/ScreenR/</a>. 
81 85
 </p>
82 86
     <pre>@Manual{,
83 87
   title = {ScreenR: Package to Perform High Throughput Biological Screening},
84 88
   author = {Emanuel Michele Soda and Elena Ceccacci},
85 89
   year = {2022},
86
-  note = {R package version 0.99.5},
90
+  note = {R package version 0.99.53},
87 91
   url = {https://emanuelsoda.github.io/ScreenR/},
88 92
 }</pre>
89 93
 
... ...
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94 98
 
95 99
 
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98 102
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99 103
 
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18 18
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
19 19
 <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
20 20
 <script src="pkgdown.js"></script><meta property="og:title" content="Package to Perform High Throughput Biological Screening">
21
-<meta property="og:description" content="ScreenR is an easy and effective package to perform hits 
22
-             identification in loss of function High Throughput Biological 
23
-             Screening performed with shRNAs library. ScreenR combines the 
24
-             power of software like edgeR with the simplicity of the Tydiverse 
25
-             metapackage. ScreenR executes a pipeline able to find candidate 
26
-             hits from barcode counts data and integrates a wide range of 
27
-             visualization for each step of the analysis.">
21
+<meta property="og:description" content="ScreenR is a package suitable to perform hit identification in loss 
22
+            of function High Throughput Biological Screenings performed using 
23
+            barcoded shRNA-based  libraries. ScreenR combines the computing 
24
+            power of software such as  edgeR with the simplicity of use of the 
25
+            Tidyverse metapackage. ScreenR executes a pipeline able to find 
26
+            candidate hits from barcode counts, and integrates a wide range of 
27
+            visualization modes for each step of the analysis.">
28 28
 <meta property="og:image" content="/logo.png">
29 29
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
30 30
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46 46
       </button>
47 47
       <span class="navbar-brand">
48 48
         <a class="navbar-link" href="index.html">ScreenR</a>
49
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
49
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
50 50
       </span>
51 51
     </div>
52 52
 
... ...
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97 97
 <!-- badges: start -->
98 98
 
99 99
 <!-- badges: end -->
100
-<p>ScreenR is an easy and effective package to perform hits identification in loss of function High Throughput Biological Screening performed with shRNAs library. ScreenR combines the power of softwares like edgeR with the semplicity of the Tydiverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts data and integrates a wide range of visualization for each step of the analysis</p>
100
+<p>ScreenR is an easy and effective package to perform hits identification in loss of function High Throughput Biological Screening performed with shRNAs library. ScreenR combines the power of software like edgeR with the simplicity of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts data and integrates a wide range of visualization for each step of the analysis</p>
101 101
 <div class="section level2">
102 102
 <h2 id="installation-instructions">Installation instructions<a class="anchor" aria-label="anchor" href="#installation-instructions"></a>
103 103
 </h2>
... ...
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181 181
 <ul class="list-unstyled">
182 182
 <li>Emanuel Michele Soda <br><small class="roles"> Author, maintainer </small>  </li>
183 183
 <li>Elena Ceccacci <br><small class="roles"> Author </small>  </li>
184
+<li>Saverio Minucci <br><small class="roles"> Funder, thesis advisor </small>  </li>
184 185
 <li><a href="authors.html">More about authors...</a></li>
185 186
 </ul>
186 187
 </div>
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195 196
 <li><a href=""><img src="https://img.shields.io/github/downloads/EmanuelSoda/ScreenR/total" alt="GitHub downloads"></a></li>
196 197
 <li><a href=""><img src="https://img.shields.io/github/last-commit/EmanuelSoda/ScreenR" alt="last commit"></a></li>
197 198
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-<li><a href=""><img src="https://img.shields.io/github/languages/top/EmanuelSoda/ScreenR" alt="Lenguage"></a></li>
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+<li><a href=""><img src="https://img.shields.io/github/languages/top/EmanuelSoda/ScreenR" alt="Language"></a></li>
199 200
 </ul>
200 201
 </div>
201 202
 
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205 206
 
206 207
       <footer><div class="copyright">
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   <p></p>
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-<p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+<p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
209 210
 </div>
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17 17
       </button>
18 18
       <span class="navbar-brand">
19 19
         <a class="navbar-link" href="../index.html">ScreenR</a>
20
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
20
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
21 21
       </span>
22 22
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@@ -58,8 +58,16 @@
58 58
     </div>
59 59
 
60 60
     <div class="section level2">
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-<h2 class="page-header" data-toc-text="0.99.5" id="screenr-0995">ScreenR 0.99.5<a class="anchor" aria-label="anchor" href="#screenr-0995"></a></h2>
62
-<ul><li>Changes in version 0.99.5:
61
+<h2 class="page-header" data-toc-text="0.99.53" id="screenr-09953">ScreenR 0.99.53<a class="anchor" aria-label="anchor" href="#screenr-09953"></a></h2>
62
+<ul><li><p>Changes in version 0.99.53:</p></li>
63
+<li><p>Update to the documentation for the example dataset as requested by the reviewer</p></li>
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+<li><p>Pushed to Bioconductor</p></li>
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+<li><p>Changes in version 0.99.52:</p></li>
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+<li><p>Pushed to Bioconductor</p></li>
67
+<li><p>Changes in version 0.99.51:</p></li>
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+<li><p>Pushed to Bioconductor</p></li>
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+<li>
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+<p>Changes in version 0.99.5:</p>
63 71
 <ul><li>Now ScreenR uses R 4.2 or above</li>
64 72
 <li>Lazy data is set to FALSE</li>
65 73
 <li>In the DESCRIPTION is now present a BugReport link</li>
... ...
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116 124
 
117 125
 
118 126
       <footer><div class="copyright">
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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120 128
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4 4
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6
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1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Count Barcode Lost — barcode_lost • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Count Barcode Lost — barcode_lost"><meta property="og:description" content="This fuction counts the number of Barcode lost during the
3
-             sequencing. A barcode is lost if it has zero mapped read."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Count number of barcode lost — barcode_lost • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of barcode lost — barcode_lost"><meta property="og:description" content="This function counts the number of barcodes lost during the
3
+             sequencing. A barcode is lost if its associated shRNA has zero
4
+             mapped read in a sample."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
4 5
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
5 6
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
6 7
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
... ...
@@ -18,7 +19,7 @@
18 19
       </button>
19 20
       <span class="navbar-brand">
20 21
         <a class="navbar-link" href="../index.html">ScreenR</a>
21
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
22
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
22 23
       </span>
23 24
     </div>
24 25
 
... ...
@@ -54,14 +55,15 @@
54 55
       </header><div class="row">
55 56
   <div class="col-md-9 contents">
56 57
     <div class="page-header">
57
-    <h1>Count Barcode Lost</h1>
58
+    <h1>Count number of barcode lost</h1>
58 59
     <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/barcode_lost.R" class="external-link"><code>R/barcode_lost.R</code></a></small>
59 60
     <div class="hidden name"><code>barcode_lost.Rd</code></div>
60 61
     </div>
61 62
 
62 63
     <div class="ref-description">
63
-    <p>This fuction counts the number of Barcode lost during the
64
-             sequencing. A barcode is lost if it has zero mapped read.</p>
64
+    <p>This function counts the number of barcodes lost during the
65
+             sequencing. A barcode is lost if its associated shRNA has zero
66
+             mapped read in a sample.</p>
65 67
     </div>
66 68
 
67 69
     <div id="ref-usage">
... ...
@@ -76,7 +78,7 @@
76 78
 </dl></div>
77 79
     <div id="value">
78 80
     <h2>Value</h2>
79
-    <p>Return a tibble containing the number of barcodes lost for each
81
+    <p>Return a tibble containing the number of barcode lost for each
80 82
         sample</p>
81 83
     </div>
82 84
 
... ...
@@ -84,7 +86,7 @@
84 86
     <h2>Examples</h2>
85 87
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">get0</a></span><span class="op">(</span><span class="st">"object"</span>, envir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html" class="external-link">asNamespace</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span><span class="op">)</span></span>
86 88
 <span class="r-in"></span>
87
-<span class="r-in"><span class="co"># In order to count the number of barcode lost just the ScreenR object is</span></span>
89
+<span class="r-in"><span class="co"># In order to count the number of barcodes lost just the ScreenR object is</span></span>
88 90
 <span class="r-in"><span class="co"># needed</span></span>
89 91
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">barcode_lost</span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span></span>
90 92
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 2</span></span>
... ...
@@ -107,7 +109,7 @@
107 109
 
108 110
 
109 111
       <footer><div class="copyright">
110
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
112
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
111 113
 </div>
112 114
 
113 115
 <div class="pkgdown">
... ...
@@ -1,5 +1,6 @@
1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute Camera — compute_camera • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute Camera — compute_camera"><meta property="og:description" content="This internal function computes the actual hits using camera."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute Camera — compute_camera • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute Camera — compute_camera"><meta property="og:description" content="This internal function computes the actual hits using  the
3
+             camera method."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
3 4
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
4 5
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
5 6
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
... ...
@@ -17,7 +18,7 @@
17 18
       </button>
18 19
       <span class="navbar-brand">
19 20
         <a class="navbar-link" href="../index.html">ScreenR</a>
20
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
21
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
21 22
       </span>
22 23
     </div>
23 24
 
... ...
@@ -59,7 +60,8 @@
59 60
     </div>
60 61
 
61 62
     <div class="ref-description">
62
-    <p>This internal function computes the actual hits using camera.</p>
63
+    <p>This internal function computes the actual hits using  the
64
+             camera method.</p>
63 65
     </div>
64 66
 
65 67
     <div id="ref-usage">
... ...
@@ -90,10 +92,11 @@ linear model analysis created using
90 92
 <code><a href="https://rdrr.io/r/stats/model.matrix.html" class="external-link">model.matrix</a></code></p></dd>
91 93
 
92 94
     <dt><code>thresh</code></dt>
93
-<dd><p>The threshold</p></dd>
95
+<dd><p>The threshold for the False Discovery Rate (FDR) that has to be
96
+used to select the statistically significant hits.</p></dd>
94 97
 
95 98
     <dt><code>lfc</code></dt>
96
-<dd><p>The Log2FC</p></dd>
99
+<dd><p>The Log2FC threshold.</p></dd>
97 100
 
98 101
     <dt><code>number_barcode</code></dt>
99 102
 <dd><p>Number of barcode that as to be differentially
... ...
@@ -118,7 +121,7 @@ number_barcode = 5 shRNA DE.</p></dd>
118 121
 
119 122
 
120 123
       <footer><div class="copyright">
121
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
124
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
122 125
 </div>
123 126
 
124 127
 <div class="pkgdown">
... ...
@@ -1,6 +1,8 @@
1 1
 <!DOCTYPE html>
2 2
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute data Table — compute_data_table • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute data Table — compute_data_table"><meta property="og:description" content="This function computes the data table that will be used
3
-             for the analysis."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
3
+             for the analysis. The data_table is a tidy and normalized
4
+             version of the original count_table and will be used
5
+             throughout the analysis."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
4 6
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
5 7
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
6 8
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
... ...
@@ -18,7 +20,7 @@
18 20
       </button>
19 21
       <span class="navbar-brand">
20 22
         <a class="navbar-link" href="../index.html">ScreenR</a>
21
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
23
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
22 24
       </span>
23 25
     </div>
24 26
 
... ...
@@ -61,7 +63,9 @@
61 63
 
62 64
     <div class="ref-description">
63 65
     <p>This function computes the data table that will be used
64
-             for the analysis.</p>
66
+             for the analysis. The data_table is a tidy and normalized
67
+             version of the original count_table and will be used
68
+             throughout the analysis.</p>
65 69
     </div>
66 70
 
67 71
     <div id="ref-usage">
... ...
@@ -103,7 +107,7 @@
103 107
 
104 108
 
105 109
       <footer><div class="copyright">
106
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
110
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
107 111
 </div>
108 112
 
109 113
 <div class="pkgdown">
... ...
@@ -1,6 +1,6 @@
1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute the Explained Variance — compute_explained_variance • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute the Explained Variance — compute_explained_variance"><meta property="og:description" content="This function compute the explained variance by each of the
3
-             Principal Components"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute explained variance — compute_explained_variance • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute explained variance — compute_explained_variance"><meta property="og:description" content="This  is an internal function  used to compute
3
+             the explained variance by each of the Principal Components."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
4 4
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
5 5
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
6 6
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
... ...
@@ -18,7 +18,7 @@
18 18
       </button>
19 19
       <span class="navbar-brand">
20 20
         <a class="navbar-link" href="../index.html">ScreenR</a>
21
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
21
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
22 22
       </span>
23 23
     </div>
24 24
 
... ...
@@ -54,14 +54,14 @@
54 54
       </header><div class="row">
55 55
   <div class="col-md-9 contents">
56 56
     <div class="page-header">
57
-    <h1>Compute the Explained Variance</h1>
57
+    <h1>Compute explained variance</h1>
58 58
     <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/plot_mds.R" class="external-link"><code>R/plot_mds.R</code></a></small>
59 59
     <div class="hidden name"><code>compute_explained_variance.Rd</code></div>
60 60
     </div>
61 61
 
62 62
     <div class="ref-description">
63
-    <p>This function compute the explained variance by each of the
64
-             Principal Components</p>
63
+    <p>This  is an internal function  used to compute
64
+             the explained variance by each of the Principal Components.</p>
65 65
     </div>
66 66
 
67 67
     <div id="ref-usage">
... ...
@@ -106,7 +106,7 @@
106 106
 
107 107
 
108 108
       <footer><div class="copyright">
109
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
109
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
110 110
 </div>
111 111
 
112 112
 <div class="pkgdown">
... ...
@@ -1,10 +1,11 @@
1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute Metrics — compute_metrics • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute Metrics — compute_metrics"><meta property="og:description" content="This function computes the  metrics that will be then used
3
-             to compute the Z-score using the function
4
-             find_zscore_hit starting from the screenR object
5
-             for a given treatment in a given day. More information can
6
-             be found at this paper
7
-             Z-score"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute Metrics — compute_metrics • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute Metrics — compute_metrics"><meta property="og:description" content="This function computes the metrics that will be then used
3
+             to compute the z-score using the function
4
+             find_zscore_hit starting from the screenr object
5
+             for a given treatment in a given day. More information about the
6
+             z-score and other metrics used in genetic screening can be found
7
+             at this paper
8
+             z-score"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
8 9
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
9 10
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
10 11
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
... ...
@@ -22,7 +23,7 @@
22 23
       </button>
23 24
       <span class="navbar-brand">
24 25
         <a class="navbar-link" href="../index.html">ScreenR</a>
25
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
26
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
26 27
       </span>
27 28
     </div>
28 29
 
... ...
@@ -64,12 +65,13 @@
64 65
     </div>
65 66
 
66 67
     <div class="ref-description">
67
-    <p>This function computes the  metrics that will be then used
68
-             to compute the Z-score using the function
69
-             <code><a href="find_zscore_hit.html">find_zscore_hit</a></code> starting from the screenR object
70
-             for a given treatment in a given day. More information can
71
-             be found at this paper
72
-             <a href="https://pubmed.ncbi.nlm.nih.gov/21515799/" class="external-link">Z-score</a></p>
68
+    <p>This function computes the metrics that will be then used
69
+             to compute the z-score using the function
70
+             <code><a href="find_zscore_hit.html">find_zscore_hit</a></code> starting from the screenr object
71
+             for a given treatment in a given day. More information about the
72
+             z-score and other metrics used in genetic screening can be found
73
+             at this paper
74
+             <a href="https://pubmed.ncbi.nlm.nih.gov/21515799/" class="external-link">z-score</a></p>
73 75
     </div>
74 76
 
75 77
     <div id="ref-usage">
... ...
@@ -82,11 +84,20 @@
82 84
 <dd><p>The ScreenR object obtained using the
83 85
 <code><a href="create_screenr_object.html">create_screenr_object</a></code></p></dd>
84 86
 <dt>control</dt>
85
-<dd><p>The vector specifying the control samples</p></dd>
87
+<dd><p>A string specifying the sample that as to be used as
88
+control in the analysis.
89
+This string has to be equal to the interested sample in the
90
+Treatment column of the data_table slot</p></dd>
86 91
 <dt>treatment</dt>
87
-<dd><p>The vector specifying the treated samples</p></dd>
92
+<dd><p>A string specifying the sample that as to be used as
93
+treatment in the analysis.
94
+This string has to be equal to the interested sample in the
95
+Treatment column of the data_table slot.</p></dd>
88 96
 <dt>day</dt>
89
-<dd><p>A string containing the day to consider</p></dd>
97
+<dd><p>A string containing the day (time point) to consider in the
98
+metrics computation.
99
+This string has to be equal to the interested sample in the
100
+Day column of the data_table slot.</p></dd>
90 101
 </dl></div>
91 102
     <div id="value">
92 103
     <h2>Value</h2>
... ...
@@ -110,7 +121,6 @@
110 121
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 1000    Gene_350   127.    130.  -<span style="color: #BB0000;">0.034</span><span style="color: #BB0000; text-decoration: underline;">4</span> -<span style="color: #BB0000;">0.077</span><span style="color: #BB0000; text-decoration: underline;">3</span>       -<span style="color: #BB0000;">0.327</span> Time3 Time3    </span>
111 122
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 10001   Gene_379   492.    463.   0.089<span style="text-decoration: underline;">5</span>  0.184         0.779 Time3 Time3    </span>
112 123
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 10002   Gene_379   147.    169.  -<span style="color: #BB0000;">0.201</span>  -<span style="color: #BB0000;">0.430</span>        -<span style="color: #BB0000;">1.82</span>  Time3 Time3    </span>
113
-<span class="r-in"></span>
114 124
 </code></pre></div>
115 125
     </div>
116 126
   </div>
... ...
@@ -121,7 +131,7 @@
121 131
 
122 132
 
123 133
       <footer><div class="copyright">
124
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
134
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
125 135
 </div>
126 136
 
127 137
 <div class="pkgdown">
... ...
@@ -18,7 +18,7 @@
18 18
       </button>
19 19
       <span class="navbar-brand">
20 20
         <a class="navbar-link" href="../index.html">ScreenR</a>
21
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
21
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
22 22
       </span>
23 23
     </div>
24 24
 
... ...
@@ -109,7 +109,7 @@ for the linear model</p></dd>
109 109
 
110 110
 
111 111
       <footer><div class="copyright">
112
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
112
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
113 113
 </div>
114 114
 
115 115
 <div class="pkgdown">
... ...
@@ -1,7 +1,9 @@
1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Count the number of mapped read — count_mapped_reads • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of mapped read — count_mapped_reads"><meta property="og:description" content="This function counts the number of reads for Barcode
3
-             in each sample. It is a quality control fuction (QC) to see if
4
-             the biological protocol went as planned."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Count the number of mapped read — count_mapped_reads • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of mapped read — count_mapped_reads"><meta property="og:description" content="This function counts the number of reads for each barcode
3
+             in each sample. It is a quality control function (QC) to see if
4
+             the biological protocol went as planned.
5
+             If a sample has very low mapped compared to the other means
6
+             that is has a lower quality."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
5 7
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
6 8
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
7 9
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
... ...
@@ -19,7 +21,7 @@
19 21
       </button>
20 22
       <span class="navbar-brand">
21 23
         <a class="navbar-link" href="../index.html">ScreenR</a>
22
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
24
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
23 25
       </span>
24 26
     </div>
25 27
 
... ...
@@ -61,9 +63,11 @@
61 63
     </div>
62 64
 
63 65
     <div class="ref-description">
64
-    <p>This function counts the number of reads for Barcode
65
-             in each sample. It is a quality control fuction (QC) to see if
66
-             the biological protocol went as planned.</p>
66
+    <p>This function counts the number of reads for each barcode
67
+             in each sample. It is a quality control function (QC) to see if
68
+             the biological protocol went as planned.
69
+             If a sample has very low mapped compared to the other means
70
+             that is has a lower quality.</p>
67 71
     </div>
68 72
 
69 73
     <div id="ref-usage">
... ...
@@ -104,7 +108,7 @@
104 108
 
105 109
 
106 110
       <footer><div class="copyright">
107
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
111
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
108 112
 </div>
109 113
 
110 114
 <div class="pkgdown">
111 115
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112 116
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1
-<!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Plot the distribution of the mapped reads — distribution_mapped_reads • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Plot the distribution of the mapped reads — distribution_mapped_reads"><meta property="og:description" content="This function creates a boxplot to show the distribution of
3
-             the mapped reads in different samples."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
4
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
5
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
6
-<![endif]--></head><body data-spy="scroll" data-target="#toc">
7
-    
8
-
9
-    <div class="container template-reference-topic">
10
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
11
-  <div class="container">
12
-    <div class="navbar-header">
13
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
14
-        <span class="sr-only">Toggle navigation</span>
15
-        <span class="icon-bar"></span>
16
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17
-        <span class="icon-bar"></span>
18
-      </button>
19
-      <span class="navbar-brand">
20
-        <a class="navbar-link" href="../index.html">ScreenR</a>
21
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
22
-      </span>
23
-    </div>
24
-
25
-    <div id="navbar" class="navbar-collapse collapse">
26
-      <ul class="nav navbar-nav"><li>
27
-  <a href="../reference/index.html">Reference</a>
28
-</li>
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30
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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-  </a>
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36
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37
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41
-</li>
42
-      </ul><ul class="nav navbar-nav navbar-right"><li>
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-  <a href="https://github.com/EmanuelSoda/ScreenR/" class="external-link">
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-  <div class="col-md-9 contents">
56
-    <div class="page-header">
57
-    <h1>Plot the distribution of the mapped reads</h1>
58
-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/distribution_mapped_reads.R" class="external-link"><code>R/distribution_mapped_reads.R</code></a></small>
59
-    <div class="hidden name"><code>distribution_mapped_reads.Rd</code></div>
60
-    </div>
61
-
62
-    <div class="ref-description">
63
-    <p>This function creates a boxplot to show the distribution of
64
-             the mapped reads in different samples.</p>
65
-    </div>
66
-
67
-    <div id="ref-usage">
68
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">distribution_mapped_reads</span><span class="op">(</span>
69
-  <span class="va">screenR_Object</span>,
70
-  palette <span class="op">=</span> <span class="cn">NULL</span>,
71
-  alpha <span class="op">=</span> <span class="fl">1</span>,
72
-  type <span class="op">=</span> <span class="st">"boxplot"</span>
73
-<span class="op">)</span></code></pre></div>
74
-    </div>
75
-
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-    <div id="arguments">
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-    <h2>Arguments</h2>
78
-    <dl><dt>screenR_Object</dt>
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-<dd><p>The ScreenR object obtained using the
80
-<code><a href="create_screenr_object.html">create_screenr_object</a></code>.</p></dd>
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-<dt>palette</dt>
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-<dd><p>The color vector for the plot.</p></dd>
83
-<dt>alpha</dt>
84
-<dd><p>A value for the opacity of the plot.
85
-Allowed values are in the range 0 to 1</p></dd>
86
-<dt>type</dt>
87
-<dd><p>The type of plot. The default is "boxplot" the other option is
88
-"density."</p></dd>
89
-</dl></div>
90
-    <div id="value">
91
-    <h2>Value</h2>
92
-    <p>Return a tibble containing the number of mapped read for sample</p>
93
-    </div>
94
-
95
-    <div id="ref-examples">
96
-    <h2>Examples</h2>
97
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">get0</a></span><span class="op">(</span><span class="st">"object"</span>, envir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html" class="external-link">asNamespace</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span><span class="op">)</span></span>
98
-<span class="r-in"></span>
99
-<span class="r-in"><span class="co"># Boxplot</span></span>
100
-<span class="r-in"><span class="fu">distribution_mapped_reads</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
101
-<span class="r-plt img"><img src="distribution_mapped_reads-1.png" alt="" width="700" height="433"></span>
102
-<span class="r-in"></span>
103
-<span class="r-in"><span class="co"># Density</span></span>
104
-<span class="r-in"><span class="fu">distribution_mapped_reads</span><span class="op">(</span><span class="va">object</span>, type <span class="op">=</span> <span class="st">"density"</span><span class="op">)</span></span>
105
-<span class="r-plt img"><img src="distribution_mapped_reads-2.png" alt="" width="700" height="433"></span>
106
-<span class="r-in"></span>
107
-<span class="r-in"><span class="fu">distribution_mapped_reads</span><span class="op">(</span><span class="va">object</span>, type <span class="op">=</span> <span class="st">"density"</span>, alpha <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span></span>
108
-<span class="r-plt img"><img src="distribution_mapped_reads-3.png" alt="" width="700" height="433"></span>
109
-<span class="r-in"></span>
110
-</code></pre></div>
111
-    </div>
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-  </div>
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-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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-    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
115
-    </nav></div>
116
-</div>
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-
118
-
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-      <footer><div class="copyright">
120
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
121
-</div>
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-
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-<div class="pkgdown">
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
125
-</div>
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-
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-      </footer></div>
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-
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-  
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-
131
-
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-  
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-
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-  </body></html>
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-
... ...
@@ -19,7 +19,7 @@
19 19
       </button>
20 20
       <span class="navbar-brand">
21 21
         <a class="navbar-link" href="../index.html">ScreenR</a>
22
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
22
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
23 23
       </span>
24 24
     </div>
25 25
 
... ...
@@ -138,7 +138,7 @@ for the linear model of the the control</p></dd>
138 138
 
139 139
 
140 140
       <footer><div class="copyright">
141
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
141
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
142 142
 </div>
143 143
 
144 144
 <div class="pkgdown">
... ...
@@ -19,7 +19,7 @@
19 19
       </button>
20 20
       <span class="navbar-brand">
21 21
         <a class="navbar-link" href="../index.html">ScreenR</a>
22
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
22
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
23 23
       </span>
24 24
     </div>
25 25
 
... ...
@@ -132,7 +132,7 @@ for the Treatment</p></dd>
132 132
 
133 133
 
134 134
       <footer><div class="copyright">
135
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
135
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
136 136
 </div>
137 137
 
138 138
 <div class="pkgdown">
... ...
@@ -1,9 +1,10 @@
1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Find Camera Hit — find_camera_hit • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Find Camera Hit — find_camera_hit"><meta property="og:description" content="This function finds the hits using the camera method is
3
-             a wrapper for the camera function.
4
-             It implements the methods by proposed by Wu and Smyth (2012).
5
-             It performs a competitive test in the sense defined by Goeman
6
-             and Buhlmann (2007). The paper can be found here
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Find Camera Hit — find_camera_hit • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Find Camera Hit — find_camera_hit"><meta property="og:description" content="This function implements the method by proposed by Wu and
3
+             Smyth (2012).
4
+             The original camera method is a gene set
5
+             test, here is applied in the contest of a genetic screening
6
+             and so it erforms a competitive barcode set test.
7
+             The paper can be found here
7 8
      CAMERA"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
8 9
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
9 10
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
... ...
@@ -22,7 +23,7 @@
22 23
       </button>
23 24
       <span class="navbar-brand">
24 25
         <a class="navbar-link" href="../index.html">ScreenR</a>
25
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
26
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
26 27
       </span>
27 28
     </div>
28 29
 
... ...
@@ -64,11 +65,12 @@
64 65
     </div>
65 66
 
66 67
     <div class="ref-description">
67
-    <p>This function finds the hits using the camera method is
68
-             a wrapper for the <code><a href="https://rdrr.io/pkg/limma/man/camera.html" class="external-link">camera</a></code> function.
69
-             It implements the methods by proposed by Wu and Smyth (2012).
70
-             It performs a competitive test in the sense defined by Goeman
71
-             and Buhlmann (2007). The paper can be found here
68
+    <p>This function implements the method by proposed by Wu and
69
+             Smyth (2012).
70
+             The original <code><a href="https://rdrr.io/pkg/limma/man/camera.html" class="external-link">camera</a></code> method is a gene set
71
+             test, here is applied in the contest of a genetic screening
72
+             and so it erforms a competitive barcode set test.
73
+             The paper can be found here
72 74
      <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458527/" class="external-link">CAMERA</a></p>
73 75
     </div>
74 76
 
... ...
@@ -95,7 +97,8 @@ linear model analysis created using
95 97
 <code><a href="https://rdrr.io/r/stats/model.matrix.html" class="external-link">model.matrix</a></code></p></dd>
96 98
 <dt>contrast</dt>
97 99
 <dd><p>A vector or a single value indicating the index or the name
98
-of the column the model_matrix wo which perform the analysis</p></dd>
100
+of the column the model_matrix with which perform the
101
+analysis</p></dd>
99 102
 <dt>number_barcode</dt>
100 103
 <dd><p>Number of barcode that as to be differentially
101 104
 expressed (DE)in order to consider the gene associated
... ...
@@ -103,16 +106,17 @@ DE. Example a gene is associated
103 106
 with 10 shRNA we consider a gene DE if it has at least
104 107
 number_barcode = 5 shRNA DE.</p></dd>
105 108
 <dt>thresh</dt>
106
-<dd><p>The threshold</p></dd>
109
+<dd><p>The threshold for the False Discovery Rate (FDR) that has to be
110
+used to select the statistically significant hits.</p></dd>
107 111
 <dt>lfc</dt>
108
-<dd><p>The Log2FC</p></dd>
112
+<dd><p>The Log2FC threshold.</p></dd>
109 113
 <dt>direction</dt>
110 114
 <dd><p>String containing the direction of the variation,
111 115
 "Down" for the down regulation "Up" for the up regulation.</p></dd>
112 116
 </dl></div>
113 117
     <div id="value">
114 118
     <h2>Value</h2>
115
-    <p>The data frame with hit find using the camera method</p>
119
+    <p>The data frame containing the hit found using the camera method</p>
116 120
     </div>
117 121
 
118 122
     <div id="ref-examples">
... ...
@@ -148,7 +152,7 @@ number_barcode = 5 shRNA DE.</p></dd>
148 152
 
149 153
 
150 154
       <footer><div class="copyright">
151
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
155
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
152 156
 </div>
153 157
 
154 158
 <div class="pkgdown">
... ...
@@ -17,7 +17,7 @@
17 17
       </button>
18 18
       <span class="navbar-brand">
19 19
         <a class="navbar-link" href="../index.html">ScreenR</a>
20
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
20
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
21 21
       </span>
22 22
     </div>
23 23
 
... ...
@@ -111,7 +111,7 @@ in the result of all the three methods.</p></dd>
111 111
 
112 112
 
113 113
       <footer><div class="copyright">
114
-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
114
+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
115 115
 </div>
116 116
 
117 117
 <div class="pkgdown">
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1 1
 <!DOCTYPE html>
2
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Find Roast Hit — find_roast_hit • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Find Roast Hit — find_roast_hit"><meta property="og:description" content="Find the hit using the Roast method"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
2
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Find Roast Hit — find_roast_hit • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Find Roast Hit — find_roast_hit"><meta property="og:description" content="Find the hit using the roast method. Roast is a competitive gene
3
+             set test which uses rotation instead of permutation. Here is
4
+             applied in a contest of a genetic screening so it perform a
5
+             barcode competitive test testing for barcode which are
6
+             differentially expressed within a gene. More information can be
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+             found in
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+          Roast"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
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59 65
     </div>
60 66
 
61 67
     <div class="ref-description">
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-    <p>Find the hit using the Roast method</p>
68
+    <p>Find the hit using the roast method. Roast is a competitive gene
69
+             set test which uses rotation instead of permutation. Here is
70
+             applied in a contest of a genetic screening so it perform a
71
+             barcode competitive test testing for barcode which are
72
+             differentially expressed within a gene. More information can be
73
+             found in
74
+          <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922896/" class="external-link">Roast</a></p>
63 75
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       <footer><div class="copyright">
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
142 154
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
120 120
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
20
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
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129 129
 
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       <footer><div class="copyright">
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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+  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci, Saverio Minucci.</p>
133 133
 </div>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ScreenR</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.5</span>
20
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.53</span>
21 21
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57 57
     </div>
58 58
 
59 59
     <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
60
-          <h2 id="object">Object <a href="#object" class="anchor" aria-hidden="true"></a></h2>
61
-          <p class="section-desc"></p><p>Function for the ScreenR Object</p>
60
+          <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" aria-hidden="true"></a></h2>
61
+          <p class="section-desc"></p>
62 62
         </th>
63 63
       </tr></tbody><tbody><tr><td>
64
-          <p><code><a href="create_edger_obj.html">create_edger_obj()</a></code> </p>
65
-        </td>
66
-        <td><p>Create EdgeR Object</p></td>
67
-      </tr><tr><td>
68
-          <p><code><a href="create_screenr_object.html">create_screenr_object()</a></code> </p>
69
-        </td>
70
-        <td><p>Create the ScreenR Object</p></td>
71
-      </tr><tr><td>
72
-          <p><code><a href="get_annotation_table.html">get_annotation_table()</a></code> </p>
73
-        </td>
74
-        <td><p>Get ScreenR annotation table</p></td>
75
-      </tr><tr><td>
76
-          <p><code><a href="get_count_table.html">get_count_table()</a></code> </p>
77
-        </td>
78
-        <td><p>Get ScreenR count table</p></td>
79
-      </tr><tr><td>
80
-          <p><code><a href="get_data_table.html">get_data_table()</a></code> </p>
81
-        </td>
82
-        <td><p>Get ScreenR data_table</p></td>
83
-      </tr><tr><td>
84
-          <p><code><a href="get_groups.html">get_groups()</a></code> </p>
85
-        </td>
86
-        <td><p>Get ScreenR groups</p></td>
87
-      </tr><tr><td>
88
-          <p><code><a href="get_normalized_count_table.html">get_normalized_count_table()</a></code> </p>
89
-        </td>
90
-        <td><p>Get ScreenR normalized_count_table</p></td>
91
-      </tr><tr><td>
92
-          <p><code><a href="get_replicates.html">get_replicates()</a></code> </p>
93
-        </td>
94
-        <td><p>Get ScreenR replicates</p></td>
95
-      </tr><tr><td>
96
-          <p><code><a href="set_annotation_table.html">set_annotation_table()</a></code> </p>
97
-        </td>
98
-        <td><p>Set ScreenR annotation table</p></td>
99
-      </tr><tr><td>
100
-          <p><code><a href="set_count_table.html">set_count_table()</a></code> </p>
101
-        </td>
102
-        <td><p>Set ScreenR count table</p></td>
103
-      </tr><tr><td>
104
-          <p><code><a href="set_data_table.html">set_data_table()</a></code> </p>
105
-        </td>
106
-        <td><p>Set ScreenR data_table</p></td>
107
-      </tr><tr><td>
108
-          <p><code><a href="set_groups.html">set_groups()</a></code> </p>
109
-        </td>
110
-        <td><p>Set ScreenR groups</p></td>
111
-      </tr><tr><td>
112
-          <p><code><a href="set_normalized_count_table.html">set_normalized_count_table()</a></code> </p>
64
+          <p><code><a href="annotation_table.html">annotation_table</a></code> </p>
113 65
         </td>
114
-        <td><p>Set ScreenR normalized_count_table</p></td>
66
+        <td><p>Table for the annotation of Barcode</p></td>
115 67
       </tr><tr><td>
116
-          <p><code><a href="set_replicates.html">set_replicates()</a></code> </p>
117
-        </td>
118
-        <td><p>Set ScreenR replicates</p></td>
119
-      </tr></tbody><tbody><tr><th colspan="2">
120
-          <h2 id="computation">Computation <a href="#computation" class="anchor" aria-hidden="true"></a></h2>
121
-          <p class="section-desc"></p><p>Function used to perform computations</p>
122
-        </th>
123
-      </tr></tbody><tbody><tr><td>
124 68
           <p><code><a href="barcode_lost.html">barcode_lost()</a></code> </p>
125 69
         </td>
126
-        <td><p>Count Barcode Lost</p></td>
70
+        <td><p>Count number of barcode lost</p></td>
127 71
       </tr><tr><td>
128 72
           <p><code><a href="compute_data_table.html">compute_data_table()</a></code> </p>
129 73
         </td>
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@@ -141,22 +85,26 @@
141 85
         </td>
142 86
         <td><p>Count the number of mapped read</p></td>
143 87
       </tr><tr><td>
144
-          <p><code><a href="mapped_reads.html">mapped_reads()</a></code> </p>
88
+          <p><code><a href="count_table.html">count_table</a></code> </p>
145 89
         </td>
146
-        <td><p>Mapped Reads</p></td>
90
+        <td><p>Table of the count table</p></td>
147 91
       </tr><tr><td>
148
-          <p><code><a href="normalize_data.html">normalize_data()</a></code> </p>
92
+          <p><code><a href="create_edger_obj.html">create_edger_obj()</a></code> </p>
149 93
         </td>
150
-        <td><p>Normalize data</p></td>
94
+        <td><p>Create edgeR Object</p></td>
151 95
       </tr><tr><td>
152
-          <p><code><a href="remove_all_zero_row.html">remove_all_zero_row()</a></code> </p>
96
+          <p><code><a href="create_screenr_object.html">create_screenr_object()</a></code> </p>
153 97
         </td>
154
-        <td><p>Remove rows that have zero count in all samples</p></td>
155
-      </tr></tbody><tbody><tr><th colspan="2">
156
-          <h2 id="find-hit">Find Hit <a href="#find-hit" class="anchor" aria-hidden="true"></a></h2>
157
-          <p class="section-desc"></p><p>Function used to find hits</p>
158
-        </th>
159
-      </tr></tbody><tbody><tr><td>
98
+        <td><p>Create the ScreenR Object</p></td>
99
+      </tr><tr><td>
100
+          <p><code><a href="filter_by_slope.html">filter_by_slope()</a></code> </p>
101
+        </td>
102
+        <td><p>Filter using the slope filter</p></td>
103
+      </tr><tr><td>
104
+          <p><code><a href="filter_by_variance.html">filter_by_variance()</a></code> </p>
105
+        </td>
106
+        <td><p>Filter using the variance filter</p></td>
107
+      </tr><tr><td>
160 108
           <p><code><a href="find_camera_hit.html">find_camera_hit()</a></code> </p>
161 109
         </td>
162 110
         <td><p>Find Camera Hit</p></td>
... ...
@@ -176,26 +124,42 @@
176 124
           <p><code><a href="find_zscore_hit.html">find_zscore_hit()</a></code> </p>
177 125
         </td>
178 126
         <td><p>Title Find Z-score Hit</p></td>
179
-      </tr></tbody><tbody><tr><th colspan="2">
180
-          <h2 id="further-optimization">Further Optimization <a href="#further-optimization" class="anchor" aria-hidden="true"></a></h2>
181
-          <p class="section-desc"></p><p>Function to further optimize the hit found</p>
182
-        </th>
183
-      </tr></tbody><tbody><tr><td>
184
-          <p><code><a href="filter_by_slope.html">filter_by_slope()</a></code> </p>
127
+      </tr><tr><td>
128
+          <p><code><a href="get_annotation_table.html">get_annotation_table()</a></code> </p>
185 129
         </td>
186
-        <td><p>Filter using the slope filter</p></td>
130
+        <td><p>Get ScreenR annotation table</p></td>
187 131
       </tr><tr><td>
188
-          <p><code><a href="filter_by_variance.html">filter_by_variance()</a></code> </p>
132
+          <p><code><a href="get_count_table.html">get_count_table()</a></code> </p>
189 133
         </td>
190
-        <td><p>Filter using the variance filter</p></td>
191
-      </tr></tbody><tbody><tr><th colspan="2">
192
-          <h2 id="plot">Plot <a href="#plot" class="anchor" aria-hidden="true"></a></h2>
193
-          <p class="section-desc"></p><p>Functions used to visualize the data</p>
194
-        </th>
195
-      </tr></tbody><tbody><tr><td>
134
+        <td><p>Get ScreenR count table</p></td>
135
+      </tr><tr><td>
136
+          <p><code><a href="get_data_table.html">get_data_table()</a></code> </p>
137
+        </td>
138
+        <td><p>Get ScreenR data_table</p></td>
139
+      </tr><tr><td>
140
+          <p><code><a href="get_groups.html">get_groups()</a></code> </p>
141
+        </td>
142
+        <td><p>Get ScreenR groups</p></td>
143
+      </tr><tr><td>
144
+          <p><code><a href="get_normalized_count_table.html">get_normalized_count_table()</a></code> </p>
145
+        </td>
146
+        <td><p>Get ScreenR normalized_count_table</p></td>
147
+      </tr><tr><td>
148
+          <p><code><a href="get_replicates.html">get_replicates()</a></code> </p>
149
+        </td>
150
+        <td><p>Get ScreenR replicates</p></td>
151
+      </tr><tr><td>
152
+          <p><code><a href="mapped_reads.html">mapped_reads()</a></code> </p>
153
+        </td>
154
+        <td><p>Mapped Reads</p></td>
155
+      </tr><tr><td>
156
+          <p><code><a href="normalize_data.html">normalize_data()</a></code> </p>
157
+        </td>
158
+        <td><p>Normalize data</p></td>
159
+      </tr><tr><td>
196 160
           <p><code><a href="plot_barcode_hit.html">plot_barcode_hit()</a></code> </p>
197 161
         </td>
198
-        <td><p>Plot Barcode Hit</p></td>
162
+        <td><p>Plot barcode hit</p></td>
199 163
       </tr><tr><td>
200 164
           <p><code><a href="plot_barcode_lost.html">plot_barcode_lost()</a></code> </p>
201 165
         </td>
... ...
@@ -203,11 +167,11 @@
203 167
       </tr><tr><td>
204 168
           <p><code><a href="plot_barcode_lost_for_gene.html">plot_barcode_lost_for_gene()</a></code> </p>
205 169
         </td>
206
-        <td><p>Plot number of barcode lost for gene</p></td>
170
+        <td><p>Plot number of barcode lost for  gene</p></td>
207 171
       </tr><tr><td>
208 172
           <p><code><a href="plot_barcode_trend.html">plot_barcode_trend()</a></code> </p>
209 173
         </td>
210
-        <td><p>Plot the trend over time of the Barcodes</p></td>
174
+        <td><p>Plot the trend over time of the barcodes</p></td>
211 175
       </tr><tr><td>
212 176
           <p><code><a href="plot_boxplot.html">plot_boxplot()</a></code> </p>
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         </td>
... ...
@@ -223,7 +187,7 @@
223 187
       </tr><tr><td>
224 188
           <p><code><a href="plot_mapped_reads.html">plot_mapped_reads()</a></code> </p>
225 189
         </td>
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-        <td><p>Plot Mapped Reads</p></td>
190
+        <td><p>Plot mapped reads</p></td>
227 191
       </tr><tr><td>
228 192
           <p><code><a href="plot_mapped_reads_distribution.html">plot_mapped_reads_distribution()</a></code> </p>
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         </td>
... ...
@@ -235,23 +199,39 @@
235 199
       </tr><tr><td>
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           <p><code><a href="plot_trend.html">plot_trend()</a></code> </p>
237 201
         </td>
238
-        <td><p>Plot the trend Hit Gene</p></td>
202
+        <td><p>Plot the trend hit gene</p></td>
239 203
       </tr><tr><td>
240 204
           <p><code><a href="plot_zscore_distribution.html">plot_zscore_distribution()</a></code> </p>
241 205
         </td>
242 206
         <td><p>Plot distribution Z-score</p></td>
243
-      </tr></tbody><tbody><tr><th colspan="2">
244
-          <h2 id="data">Data <a href="#data" class="anchor" aria-hidden="true"></a></h2>