mutualExclusivity_functionR.txt

mutualExclusivity <- function(x) {
	myOut <- data.frame(OR=double(),p.value=double())
	for (i in 1:nrow(x)) {
		for (j in 1:nrow(x)) {
			mymat = matrix(0,2,2)
			gene1 <- rownames(x[i,,drop=F])[1]
			gene2 <- rownames(x[j,,drop=F])[1]
			if (gene1 != gene2) {
			genes <- c(gene1, gene2)
			comparison <- paste(genes[order(genes)], collapse=".")
			message(paste("Comparing",comparison,"..."))
			if(!(comparison %in% myOut[comparison,])) {
				for (k in 1:ncol(x)) {
				message(colnames(x[,k,drop=F]))
					if (sum(x[c(i,j),k]) == 2) {
						mymat[1,1] <- mymat[1,1]+1
					} else if (x[j,k] == 1) {
						mymat[2,1] <- mymat[2,1]+1
					} else if (x[i,k] == 1) {
						mymat[1,2] <- mymat[1,2]+1
					} else {
						mymat[2,2] <- mymat[2,2]+1
					}
				}
				pvalue <- fisher.test(mymat)$p.value
				OR <- log((mymat[2,2]*mymat[1,1])/(mymat[1,2]*mymat[2,1]))
				myOut[comparison,] <- c(OR, pvalue)
				}
			}
		}
	}
	return(myOut)
}