% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/runGSVA.R
 \name{runGSVA}
 \alias{runGSVA}
 \title{Run GSVA analysis on a \linkS4class{SingleCellExperiment} object}
 \usage{
 runGSVA(
   inSCE,
   useAssay = "logcounts",
   resultNamePrefix = NULL,
   geneSetCollectionName,
   ...
 )
 }
 \arguments{
 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}
 
 \item{useAssay}{Indicate which assay to use. The default is "logcounts"}
 

 \item{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}.}

 \item{geneSetCollectionName}{Character. The name of the gene set collection 
 to use.}

 
 \item{...}{Parameters to pass to gsva()}
 }
 \value{

 A \linkS4class{SingleCellExperiment} object with pathway activity 
 scores from GSVA stored in \code{reducedDim} as 
 \code{GSVA_geneSetCollectionName_Scores}.

 }
 \description{
 Run GSVA analysis on a \linkS4class{SingleCellExperiment} object
 }
 \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")

 }