Browse code

[FIX] Fixed issues in documentation

Giulia Pais authored on 21/10/2021 17:35:24
Showing 5 changed files

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@@ -1,6 +1,6 @@
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 Package: ISAnalytics
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 Title: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
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-Version: 1.3.7
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+Version: 1.3.8
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 Date: 2020-07-03
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 Authors@R: c(
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   person(given = "Andrea",
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@@ -1110,8 +1110,8 @@ cumulative_count_union <- function(x,
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 #' data("integration_matrices", package = "ISAnalytics")
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 #' data("association_file", package = "ISAnalytics")
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 #' aggreg <- aggregate_values_by_key(
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-#'     x = rlang::current_env()$integration_matrices,
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-#'     association_file = rlang::current_env()$association_file,
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+#'     x = integration_matrices,
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+#'     association_file = association_file,
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 #'     value_cols = c("seqCount", "fragmentEstimate")
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 #' )
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 #' cumulated_is <- cumulative_is(aggreg)
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@@ -1541,8 +1541,8 @@ is_sharing <- function(...,
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 #' data("integration_matrices", package = "ISAnalytics")
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 #' data("association_file", package = "ISAnalytics")
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 #' aggreg <- aggregate_values_by_key(
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-#'     x = rlang::current_env()$integration_matrices,
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-#'     association_file = rlang::current_env()$association_file,
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+#'     x = integration_matrices,
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+#'     association_file = association_file,
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 #'     value_cols = c("seqCount", "fragmentEstimate")
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 #' )
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 #' filtered_by_purity <- purity_filter(
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@@ -1759,8 +1759,8 @@ purity_filter <- function(x,
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 #' data("integration_matrices", package = "ISAnalytics")
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 #' data("association_file", package = "ISAnalytics")
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 #' aggreg <- aggregate_values_by_key(
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-#'     x = rlang::current_env()$integration_matrices,
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-#'     association_file = rlang::current_env()$association_file,
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+#'     x = integration_matrices,
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+#'     association_file = association_file,
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 #'     value_cols = c("seqCount", "fragmentEstimate")
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 #' )
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 #' df1 <- aggreg %>%
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@@ -1769,15 +1769,11 @@ purity_filter <- function(x,
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 #'     dplyr::filter(.data$Tissue == "PB")
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 #' source <- iss_source(df1, df2)
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 #' source
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-#' ggplot2::ggplot(source$PT001, ggplot2::aes(
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-#'     x = as.factor(g2_TimePoint),
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-#'     y = sharing_perc, fill = g1
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-#' )) +
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+#' ggplot2::ggplot(source$PT001, ggplot2::aes(x = as.factor(g2_TimePoint),
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+#'                                            y = sharing_perc, fill = g1)) +
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 #'     ggplot2::geom_col() +
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-#'     ggplot2::labs(
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-#'         x = "Time point", y = "Shared IS % with MNC BM",
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-#'         title = "Source of is MNC BM vs MNC PB"
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-#'     )
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+#'     ggplot2::labs(x = "Time point", y = "Shared IS % with MNC BM",
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+#'                   title = "Source of is MNC BM vs MNC PB")
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 iss_source <- function(reference,
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     selection,
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     ref_group_key = c(
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@@ -43,8 +43,8 @@ time point "t+1".
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 data("integration_matrices", package = "ISAnalytics")
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 data("association_file", package = "ISAnalytics")
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 aggreg <- aggregate_values_by_key(
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-    x = rlang::current_env()$integration_matrices,
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-    association_file = rlang::current_env()$association_file,
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+    x = integration_matrices,
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+    association_file = association_file,
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     value_cols = c("seqCount", "fragmentEstimate")
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 )
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 cumulated_is <- cumulative_is(aggreg)
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@@ -52,8 +52,8 @@ observed for the first time.
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 data("integration_matrices", package = "ISAnalytics")
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 data("association_file", package = "ISAnalytics")
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 aggreg <- aggregate_values_by_key(
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-    x = rlang::current_env()$integration_matrices,
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-    association_file = rlang::current_env()$association_file,
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+    x = integration_matrices,
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+    association_file = association_file,
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     value_cols = c("seqCount", "fragmentEstimate")
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 )
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 df1 <- aggreg \%>\%
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@@ -104,8 +104,8 @@ identified by the rows in the provided data frame are processed.
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 data("integration_matrices", package = "ISAnalytics")
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 data("association_file", package = "ISAnalytics")
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 aggreg <- aggregate_values_by_key(
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-    x = rlang::current_env()$integration_matrices,
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-    association_file = rlang::current_env()$association_file,
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+    x = integration_matrices,
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+    association_file = association_file,
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     value_cols = c("seqCount", "fragmentEstimate")
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 )
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 filtered_by_purity <- purity_filter(