R/runGSVA.R

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

#' Run GSVA analysis on a \linkS4class{SingleCellExperiment} object
#'
#' @param inSCE Input \linkS4class{SingleCellExperiment} object.
#' @param useAssay Indicate which assay to use. The default is "logcounts"
#' @param geneSetCollectionName Character. The name of the gene set collection 
#' to use. 
#' @param resultNamePrefix  Character. Prefix to the name the GSVA results 
#' which will be stored in the reducedDim slot of \code{inSCE}. The names of the 
#' output matrix will be \code{resultNamePrefix_Scores}. If this parameter is 
#' set to \code{NULL}, then "GSVA_geneSetCollectionName_" will be used. Default 
#' \code{NULL}.
#' @param ... Parameters to pass to gsva()
#'
#' @return A \linkS4class{SingleCellExperiment} object with pathway activity 
#' scores from GSVA stored in \code{reducedDim} as 
#' \code{GSVA_geneSetCollectionName_Scores}.
#' @export
#' @examples
#' data(scExample, package = "singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- scaterlogNormCounts(sce, assayName = "logcounts")
#' gs1 <- rownames(sce)[seq(10)]
#' gs2 <- rownames(sce)[seq(11,20)]
#' gs <- list("geneset1" = gs1, "geneset2" = gs2)
#' 
#' sce <- importGeneSetsFromList(inSCE = sce,geneSetList = gs,
#'                                            by = "rownames")
#' sce <- runGSVA(inSCE = sce, 
#'                geneSetCollectionName = "GeneSetCollection", 
#'                useAssay = "logcounts")
runGSVA <- function(inSCE, useAssay = "logcounts",
                    resultNamePrefix = NULL, geneSetCollectionName, ...){
  gsvaRes <- NULL
  gene.Set <- .getGeneSetCollection(inSCE, geneSetCollectionName)
  
  message(date(), " ... Running GSVA")

  gsvaData <- as.matrix(expData(inSCE, useAssay))
  gsvaPar <- GSVA::gsvaParam(gsvaData, gene.Set)
  gsvaRes <- t(GSVA::gsva(gsvaPar))
  
  if(is.null(resultNamePrefix)) {
    resultNamePrefix <- paste0("GSVA_", geneSetCollectionName, "_")
  }
  
  SingleCellExperiment::reducedDim(inSCE, 
                                   paste0(resultNamePrefix, 
                                          "Scores")) <- gsvaRes 
  
  if ("pathwayAnalysisResultNames" %in% names(S4Vectors::metadata(inSCE))) {
    S4Vectors::metadata(inSCE)[["pathwayAnalysisResultNames"]] <- 
      c(S4Vectors::metadata(inSCE)[["pathwayAnalysisResultNames"]],
        paste0(resultNamePrefix, "Scores"))
  } else {
    S4Vectors::metadata(inSCE)[["pathwayAnalysisResultNames"]] <- 
      c(paste0(resultNamePrefix, "Scores"))
  }

  return(inSCE)
}