Nothing

```
##This function performs pairwise GSEA: it looks for gene sets that are
##specifically over-represented towards the 2 different ends of two
##ranked lists of genes, in a gene set collection.
pairwiseGsea <- function(gl1, gl2, gsc, exponent = 1, nPermutations = 1000,
minGeneSetSize = 15, pAdjustMethod = "BH") {
##check arguments
paraCheck("genelist", gl1)
paraCheck("genelist", gl2)
paraCheck("gsc", gsc)
paraCheck("exponent", exponent)
paraCheck("nPermutations", nPermutations)
paraCheck("minGeneSetSize", minGeneSetSize)
paraCheck("pAdjustMethod", pAdjustMethod)
##Check that the two phenotype vectors contain data on the same genes
if(!all(names(gl1) == names(gl2)))
stop("The two phenotypes must be measured on the same genes")
##The collectionGsea function will test that the other parameters
##have the right format
##Compute the individual enrichment scores and permutation based scores
collGsea.ph1 <- collectionGsea(collectionOfGeneSets = gsc,
geneList = gl1, exponent = exponent, nPermutations = nPermutations,
minGeneSetSize = minGeneSetSize)
collGsea.ph2 <- collectionGsea(collectionOfGeneSets = gsc,
geneList = gl2, exponent = exponent, nPermutations = nPermutations,
minGeneSetSize = minGeneSetSize)
##Compute the differences between scores
mPh.Obs.Scores <- collGsea.ph1$Observed.scores - collGsea.ph2$Observed.scores
names(mPh.Obs.Scores) <- names(collGsea.ph1$Observed.scores)
mPH.Perm.Scores <- collGsea.ph1$Permutation.scores - collGsea.ph2$Permutation.scores
rownames(mPH.Perm.Scores) <- rownames(collGsea.ph1$Permutation.scores)
##Compute the p values
mPh.Obs.Scores2 <- abs(mPh.Obs.Scores)
mPh.pvalue2 <- sapply(1:length(gsc), function(i) {
sum(abs(mPH.Perm.Scores[i,]) > mPh.Obs.Scores2[i]) /
length(mPH.Perm.Scores[i,])
})
names(mPh.pvalue2) <- names(mPh.Obs.Scores)
##Produce the results table
a.pval2 <- p.adjust(mPh.pvalue2, method = pAdjustMethod)
mPh.table2 <- cbind(collGsea.ph1$Observed.scores,
collGsea.ph2$Observed.scores, mPh.pvalue2, a.pval2)
rownames(mPh.table2) <- names(mPh.pvalue2)
colnames(mPh.table2) <- c("ES.phenotype1", "ES.phenotype2",
"P.value", "Adjusted.P.value")
mPh.table2 <- mPh.table2[order(mPh.pvalue2), ]
}
```

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