Translate part of `enrichment()` to C++

[wleoncio]

This loop, specifically:

EnrichIntersect/R/enrichment.R

Lines 110 to 182 in 988c05e

	for (k in 1:n_groups) { # group index
	idx <- rep(NA, n)
	for (j in 1:n) {
	idx[j] <- names(myList[j]) %in%
	custom.set[custom.set$group == groups[k], 1]
	}
	if (sum(idx)) {
	F1 <- cumsum(abs(myList)^alpha * as.numeric(idx)) /
	sum(abs(myList)^alpha * as.numeric(idx))
	F2 <- cumsum(as.numeric(!idx)) /
	(n - sum(custom.set$group == groups[k] &
	features %in% names(myList)))
	S[i, k] <- max(F1 - F2, na.rm = TRUE)
	} else {
	S[i, k] <- NA
	}
	# permutation test
	permute_S <- rep(NA, permute.n)
	for (permute_i in 1:permute.n) {
	permutationIdx <- sample(1:n, n) # n removes missing spearman's x
	myList_permute <- myList
	names(myList_permute) <- names(myList)[permutationIdx]
	for (j in 1:n) {
	idx[j] <- names(myList_permute[j]) %in%
	custom.set[custom.set$group == groups[k], 1]
	}
	if (sum(idx)) {
	F1 <- cumsum(abs(myList_permute)^alpha * as.numeric(idx)) /
	sum(abs(myList_permute)^alpha * as.numeric(idx))
	F2 <- cumsum(as.numeric(!idx)) /
	(n - sum(custom.set$group == groups[k] &
	features %in% names(myList)))
	permute_S[permute_i] <- max(F1 - F2, na.rm = TRUE)
	}
	}
	## i) p-value for enrichment score
	pvalue[i, k] <- sum(permute_S >= S[i, k], na.rm = TRUE) /
	(permute.n - sum(is.na(permute_S)))
	## ii) normalized enrichment score
	if (normalize) {
	S_norm <- S
	if (!is.na(S[i, k])) {
	if (S[i, k] >= 0) {
	S_norm[i, k] <-
	S[i, k] / mean(permute_S[permute_S >= 0], na.rm = TRUE)
	} else {
	S_norm[i, k] <-
	S[i, k] / mean(permute_S[permute_S < 0], na.rm = TRUE)
	}
	}
	S <- S_norm
	permute_S_norm <- rep(NA, permute.n)
	for (permute_i in 1:permute.n) {
	if (!is.na(permute_S[permute_i])) {
	if (permute_S[permute_i] >= 0) {
	permute_S_norm[permute_i] <- permute_S[permute_i] /
	mean(permute_S[permute_S >= 0], na.rm = TRUE)
	} else {
	permute_S_norm[permute_i] <- permute_S[permute_i] /
	mean(permute_S[permute_S < 0], na.rm = TRUE)
	}
	}
	}
	pvalue[i, k] <- sum(permute_S_norm >= S_norm[i, k], na.rm = TRUE) /
	(permute.n - sum(is.na(permute_S_norm)))
	}
	}