Nothing
topSplices <- function(fgObj, n=20, plm=NULL, cls=NULL) {
x <- matrix(rank( -fgObj$firmaGeneScores), nc=ncol(fgObj$firmaGeneScores), dimnames=dimnames(fgObj$mufScores))
z <- which( x <= n, arr.ind=TRUE)
rn <- rownames(z)
zz <- data.frame(ID=rownames(z),Sample=colnames(fgObj$firmaGeneScores)[z[,2]],Score=0)
for(i in 1:nrow(z))
zz[i,"Score"] <- fgObj$firmaGeneScores[ rn[i], z[i,"col"]]
if( !is.null(plm) & !is.null(cls) ) {
mmP <- mufMaxPositions(plm, cls, as.character(zz$ID), as.character(zz$Sample), verbose=FALSE)
zz <- cbind(zz, mmP[,-c(1:2)])
}
o <- order(zz$Score,decreasing=TRUE)
zz[o,]
}
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