Nothing

```
##This function computes enrichment scores for GSEA, running score and
##position of hits for a gene set.
gseaScores <- function(geneList, geneSet, exponent=1, mode="score") {
##check arguments
paraCheck("genelist", geneList)
paraCheck("exponent", exponent)
paraCheck("gs", geneSet)
paraCheck("gseaScore.mode", mode)
##The geneSet should be a subset of the gene universe, i.e. we keep
##only those element of the gene set that appear in the geneList
geneSet<-intersect(names(geneList), geneSet)
##Compute the size of the gene set and of the genelist
nh <- length(geneSet)
N <- length(geneList)
##Initialize the ES, runningES and the Phit and Pmiss by position
##(the actual values of Phit and Pmiss are actually cumulative sums
##of these 'by position' values)
ES <- 0
Phit <- rep(0, N)
Pmiss <- rep(0, N)
runningES <- rep(0, N)
##Stop if the geneSet is larger than the gene universe
if(nh > N) {
stop("Gene Set is larger than Gene List")
} else {
##Compute the positions of the hits in the geneList (0 if there
##is no match, 1 if there is a match)
hits <- rep(FALSE, N)
hits[which(!is.na(match(names(geneList), geneSet)))] <- TRUE
##If sum(hits)=0 then there is no match between geneList and
##geneSet, and all scores stay at 0.
if(sum(hits)!=0) {
##Fill the Phit by position
Phit[which(hits)]<-abs(geneList[which(hits)])^exponent
NR=sum(Phit)
##Fill the Pmiss by positions
Pmiss[which(!hits)]<-1/(N-nh)
##Do the cumulative sums and compute the runningES
Phit=cumsum(Phit/NR)
Pmiss=cumsum(Pmiss)
runningES<-Phit-Pmiss
##Compute the maximal (positive) and minimal (or maximal
##negative) values of the ES, and choose which one is kept
ESmax<-max(runningES)
ESmin<-min(runningES)
ES<-ifelse(abs(ESmin)>abs(ESmax), ESmin, ESmax)
}
}
##Return the relevant information according to mode
if(mode=="score")
return(ES)
if(mode=="graph")
return(list("enrichmentScore"=ES, "runningScore"=runningES,
"positions"=as.integer(hits)))
}
```

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