Nothing
`calculateFDR` <-
function(observed, permuted, progress) {
observed <- abs(observed)
permuted <- abs(permuted)
ord <- order(observed, decreasing=TRUE, na.last=TRUE)
a <- observed[ord]
A <- matrix(NA, nrow=length(a), ncol=ncol(permuted))
if (progress) pb <- txtProgressBar(min=0, max=ncol(A), style=3)
for(i in seq_len(ncol(A))) {
a.rand <- sort(permuted[,i], decreasing=TRUE, na.last=TRUE)
n.bigger <- biggerN(a, a.rand)
A[ord,i] <- n.bigger/seq_along(a)
if (progress) setTxtProgressBar(pb, i)
}
if (progress) close(pb)
FDR <- apply(A, 1, median)
FDR[FDR>1] <- 1
FDR[ord] <- rev(sapply(length(FDR):1, function(x) return(min(FDR[ord][x:length(FDR)]))))
return(FDR)
}
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