diff --git a/DESCRIPTION b/DESCRIPTION index 2ec1b7b..a74d67d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: GSVA -Version: 1.50.3 +Version: 1.50.4 Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), @@ -22,4 +22,4 @@ BugReports: https://github.com/rcastelo/GSVA/issues Encoding: UTF-8 biocViews: FunctionalGenomics, Microarray, RNASeq, Pathways, GeneSetEnrichment Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 diff --git a/R/AllClasses.R b/R/AllClasses.R index 2b8ad4a..d014ea5 100644 --- a/R/AllClasses.R +++ b/R/AllClasses.R @@ -6,7 +6,7 @@ #' Virtual superclass of expression data classes supported by `GSVA`. #' #' `GSVA` supports expression data matrices in a growing number of containers -#' and representations. This class union allows to store any of these in a slot +#' and representations. This class union allows to store any of these in a slot #' of another class as well as defining common methods for all of them. #' #' @seealso @@ -17,6 +17,7 @@ #' [`SingleCellExperiment-class`], #' [`HDF5Array`] #' +#' @aliases GsvaExprData #' @name GsvaExprData-class #' @rdname GsvaExprData-class #' @exportClass GsvaExprData diff --git a/R/gsvaParam.R b/R/gsvaParam.R index 8817c7d..14f8a8d 100644 --- a/R/gsvaParam.R +++ b/R/gsvaParam.R @@ -8,7 +8,8 @@ #' gene sets, `GSVA` takes four method-specific parameters as described below. #' #' @param exprData The expression data. Must be one of the classes -#' supported by [`GsvaExprData-class`]. +#' supported by [`GsvaExprData-class`]. Type `help(GsvaExprData)` to consult +#' the available classes. #' #' @param geneSets The gene sets. Must be one of the classes supported by #' [`GsvaGeneSets-class`]. diff --git a/R/plageParam.R b/R/plageParam.R index 8f117f3..7edd114 100644 --- a/R/plageParam.R +++ b/R/plageParam.R @@ -8,7 +8,8 @@ #' an expression data set and a collection of gene sets. #' #' @param exprData The expression data. Must be one of the classes -#' supported by [`GsvaExprData-class`]. +#' supported by [`GsvaExprData-class`]. Type `help(GsvaExprData)` to consult +#' the available classes. #' #' @param geneSets The gene sets. Must be one of the classes supported by #' [`GsvaGeneSets-class`]. diff --git a/R/ssgseaParam.R b/R/ssgseaParam.R index 0bf2add..e351ce2 100644 --- a/R/ssgseaParam.R +++ b/R/ssgseaParam.R @@ -8,7 +8,8 @@ #' gene sets, `ssGSEA` takes two method-specific parameters as described below. #' #' @param exprData The expression data. Must be one of the classes -#' supported by [`GsvaExprData-class`]. +#' supported by [`GsvaExprData-class`]. Type `help(GsvaExprData)` to consult +#' the available classes. #' #' @param geneSets The gene sets. Must be one of the classes supported by #' [`GsvaGeneSets-class`]. diff --git a/R/zscoreParam.R b/R/zscoreParam.R index bcd830d..1883e1e 100644 --- a/R/zscoreParam.R +++ b/R/zscoreParam.R @@ -9,7 +9,8 @@ #' sets. #' #' @param exprData The expression data. Must be one of the classes -#' supported by [`GsvaExprData-class`]. +#' supported by [`GsvaExprData-class`]. Type `help(GsvaExprData)` to consult +#' the available classes. #' #' @param geneSets The gene sets. Must be one of the classes supported by #' [`GsvaGeneSets-class`]. diff --git a/man/GsvaExprData-class.Rd b/man/GsvaExprData-class.Rd index 47d51d6..d3c735d 100644 --- a/man/GsvaExprData-class.Rd +++ b/man/GsvaExprData-class.Rd @@ -3,13 +3,14 @@ \docType{class} \name{GsvaExprData-class} \alias{GsvaExprData-class} +\alias{GsvaExprData} \title{\code{GsvaExprData} class} \description{ Virtual superclass of expression data classes supported by \code{GSVA}. } \details{ \code{GSVA} supports expression data matrices in a growing number of containers -and representations. This class union allows to store any of these in a slot +and representations. This class union allows to store any of these in a slot of another class as well as defining common methods for all of them. } \seealso{ diff --git a/man/gsvaParam-class.Rd b/man/gsvaParam-class.Rd index bb2b691..e11c84f 100644 --- a/man/gsvaParam-class.Rd +++ b/man/gsvaParam-class.Rd @@ -21,7 +21,8 @@ gsvaParam( } \arguments{ \item{exprData}{The expression data. Must be one of the classes -supported by \code{\linkS4class{GsvaExprData}}.} +supported by \code{\linkS4class{GsvaExprData}}. Type \code{help(GsvaExprData)} to consult +the available classes.} \item{geneSets}{The gene sets. Must be one of the classes supported by \code{\linkS4class{GsvaGeneSets}}.} diff --git a/man/plageParam-class.Rd b/man/plageParam-class.Rd index d25695c..40ebee4 100644 --- a/man/plageParam-class.Rd +++ b/man/plageParam-class.Rd @@ -17,7 +17,8 @@ plageParam( } \arguments{ \item{exprData}{The expression data. Must be one of the classes -supported by \code{\linkS4class{GsvaExprData}}.} +supported by \code{\linkS4class{GsvaExprData}}. Type \code{help(GsvaExprData)} to consult +the available classes.} \item{geneSets}{The gene sets. Must be one of the classes supported by \code{\linkS4class{GsvaGeneSets}}.} diff --git a/man/ssgseaParam-class.Rd b/man/ssgseaParam-class.Rd index 7d96497..759a2c9 100644 --- a/man/ssgseaParam-class.Rd +++ b/man/ssgseaParam-class.Rd @@ -19,7 +19,8 @@ ssgseaParam( } \arguments{ \item{exprData}{The expression data. Must be one of the classes -supported by \code{\linkS4class{GsvaExprData}}.} +supported by \code{\linkS4class{GsvaExprData}}. Type \code{help(GsvaExprData)} to consult +the available classes.} \item{geneSets}{The gene sets. Must be one of the classes supported by \code{\linkS4class{GsvaGeneSets}}.} diff --git a/man/zscoreParam-class.Rd b/man/zscoreParam-class.Rd index 46cc3b8..7a2eec3 100644 --- a/man/zscoreParam-class.Rd +++ b/man/zscoreParam-class.Rd @@ -17,7 +17,8 @@ zscoreParam( } \arguments{ \item{exprData}{The expression data. Must be one of the classes -supported by \code{\linkS4class{GsvaExprData}}.} +supported by \code{\linkS4class{GsvaExprData}}. Type \code{help(GsvaExprData)} to consult +the available classes.} \item{geneSets}{The gene sets. Must be one of the classes supported by \code{\linkS4class{GsvaGeneSets}}.}