Browse code

version 0.99.7

miccec authored on 13/03/2020 18:09:18
Showing15 changed files

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 Package: scTHI
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-Title:  Indentification of  significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. 
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-Version:  0.99.6
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+Title:  Indentification of  significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
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+Version:  0.99.7
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 Authors@R: c(person("Francesca Pia", "Caruso", email = "francescapia.caruso@gmail.com", role = c("aut")),
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 	person("Michele", "Ceccarelli", email = "m.ceccarelli@gmail.com", role = c("aut", "cre")))
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 Description: scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.
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-Depends: scTHI.data, R (>= 4.0)
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+Depends:  R (>= 4.0)
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 License: GPL-2
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 Encoding: UTF-8
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 RoxygenNote: 6.1.1.9000
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 LazyData: false
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 Imports: BiocParallel, Rtsne, grDevices, graphics, stats 
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-Suggests: knitr, rmarkdown
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+Suggests: scTHI.data, knitr, rmarkdown
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 VignetteBuilder: knitr
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 biocViews: Software,SingleCell
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 BugReports: https://github.com/miccec/scTHI/issues
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 #'  a specific
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 #'   phenotype based on the first significant enriched gene set.
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 #' @examples
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' Class <- TME_classification(scExample)
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 #' @return A list with two items: Class (character) and ClassLegend
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 #' @param Class Object returned by TME_classification function.
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 #' @param cexPoint Set the point size.
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 #' @examples
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' result <-  scTHI_score(scExample,
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 #'            cellCusterA = colnames(scExample)[1:30],
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 #' @param cexPoint Set the point size.
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 #' @param legendPos Character string to custom the legend position.
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 #' @examples
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' result <-  scTHI_score(scExample,
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 #'                        cellCusterA = colnames(scExample)[1:30],
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@@ -98,6 +98,7 @@ getcolors <- function(genesToplot, expMat,
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 #' @param cexPoint Set the point size.
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 #' @param interactionToplot Interaction pair to plot.
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 #' @examples
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' result <-  scTHI_score(scExample,
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 #'                  cellCusterA = colnames(scExample)[1:30],
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@@ -13,6 +13,7 @@
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 #'   and partnerB gene, respectively.
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 #' @param nRes Number of pairs to plot (all if NULL).
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 #' @examples
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' result <-  scTHI_score(scExample,
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 #'                        cellCusterA = colnames(scExample)[1:30],
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@@ -4,6 +4,7 @@
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 #' package.
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 #' @param scTHIresult scTHI object.
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 #' @examples
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' result <-  scTHI_score(scExample,
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 #'                        cellCusterA = colnames(scExample)[1:30],
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@@ -129,6 +129,7 @@ getScore <- function(expMat, interaction_table, cellCuster,
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 #' @examples
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 #'
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 #' ####################### example of scTHI_score
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+#' library(scTHI.data)
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 #' data(scExample)
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 #' result <-  scTHI_score(scExample,
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 #'       cellCusterA = colnames(scExample)[1:30],
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 of signatures of different cell types.
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 }
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 \examples{
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+library(scTHI.data)
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 data(scExample)
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 Class <- TME_classification(scExample)
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 }
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@@ -21,6 +21,7 @@ Generates a plot on the t-SNE coordinates, labeling cells by TME
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 classification.
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 }
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 \examples{
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+library(scTHI.data)
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 data(scExample)
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 result <-  scTHI_score(scExample,
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            cellCusterA = colnames(scExample)[1:30],
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 Graphs the output of scTHI_runTsne, labeling cells by clusters.
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 }
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 \examples{
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+library(scTHI.data)
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 data(scExample)
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 result <-  scTHI_score(scExample,
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                        cellCusterA = colnames(scExample)[1:30],
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 gene expression value.
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 }
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 \examples{
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+library(scTHI.data)
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 data(scExample)
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 result <-  scTHI_score(scExample,
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                  cellCusterA = colnames(scExample)[1:30],
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 Creates barplots of scTHI_score results.
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 }
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 \examples{
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+library(scTHI.data)
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 data(scExample)
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 result <-  scTHI_score(scExample,
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                        cellCusterA = colnames(scExample)[1:30],
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 package.
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 }
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 \examples{
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+library(scTHI.data)
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 data(scExample)
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 result <-  scTHI_score(scExample,
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                        cellCusterA = colnames(scExample)[1:30],
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 \examples{
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 ####################### example of scTHI_score
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+library(scTHI.data)
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 data(scExample)
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 result <-  scTHI_score(scExample,
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       cellCusterA = colnames(scExample)[1:30],