# ssgsea of the count matrix using normalized count data
# method parameter is the same as gsva from gsva package
# enrichment : transcription factors (tfs), pathways (pws), default tfs
library(GSVA) # gsva
library(GSEABase) # getGmt
funEnrichment <- function(countMatrix, scData, fun2enrich="tfs"){
normData <- preprocessCountMatrix(countMatrix, scData="TRUE")
if(fun2enrich=="tfs"){
annots <- getGmt("data/c3.tft.v6.1.entrez.gmt")
enrichTest <- gsva(expr=data.matrix(normData), gset.idx.list=annots)
} else if(fun2enrich=="pws"){
annots <- getGmt("data/")
enrichTest <- gsva(expr=data.matrix(normData), gset.idx.list=annots)
}
return(enrichTest)
}
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