Nothing
testMutationalPatternAll <- function (mtx, PRINT=FALSE) {
mtx <- mtx+1
ngenes <- ncol (mtx)
gene1.ind <- unlist (mapply (seq.int, 1, 1:(ngenes-1)))
gene2.ind <- unlist (mapply (rep, 2:ngenes, 1:(ngenes-1)))
mtx.ind.tmp <- cbind (gene1.ind, gene2.ind)
pvalues <- t(apply (mtx.ind.tmp, 1, testMutationalPatternPair, mtx=mtx, PRINT=PRINT))
colnames (pvalues) <- c("pValueLL", "pValueGL", "pValueLG", "pValueGG", "pValueME")
pvalues <- data.frame (gene1=colnames(mtx)[mtx.ind.tmp[,1]], gene2=colnames(mtx)[mtx.ind.tmp[,2]], pvalues)
return (pvalues)
}
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