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#### q-value
bh.fdr <- function(p){
# This function computes q-values using Benjamini and Hochberg's (1995)
# approach for controlling FDR.
# Author: Dan Nettleton
m <- length(p)
# k <- 1:m
ord <- order(p)
p[ord] <- (p[ord] * m) / (1:m)
qval <- p
for(i in (m - 1):1) {
qval[ord[i]] <- min(c(qval[ord[i]], qval[ord[i + 1]]))
}
return(qval)
} # End of bh.fdr().
by.fdr <- function(p){
# This function computes q-values using Benjamini and Yekutieli's (2001)
# approach for controlling FDR.
# Author: Wei-Chen Chen
m <- length(p)
hs <- sum(1 / (1:m)) # harmonic sum
ord <- order(p)
p[ord] <- (p[ord] * m * hs) / (1:m)
qval <- p
for(i in (m - 1):1) {
qval[ord[i]] <- min(c(qval[ord[i]], qval[ord[i + 1]]))
}
qval[qval > 1] <- 1
qval[qval < 0] <- 0
return(qval)
} # End of by.fdr().
qvalue <- function(p, method = c("BH1995", "BY2001")){
ret <- p
id.ok <- (!is.na(ret)) & (ret >= 0) & (ret <= 1)
if(method[1] == "BH1995"){
ret[id.ok] <- bh.fdr(ret[id.ok])
} else{
ret[id.ok] <- by.fdr(ret[id.ok])
}
ret[!id.ok] <- NaN
ret
} # End of qvalue().
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