Nothing
# TODO: TV naming of the function (BH while all sorts of tests)
IsoTestBH <- function (rp, FDR, type = c("BH", "BY"),
stat = c("E2", "Williams", "Marcus", "M", "ModifM")){
type <- match.arg(type)
stat <- match.arg(stat)
Probe.ID <- rp[,1]
rpraw <- switch(stat,
E2 = rp[,2],
Williams = rp[,3],
Marcus = rp[,4],
M = rp[,5],
ModifM = rp[,6])
## procs <- c("BH", "BY") # only "BH" and "BY" are needed
## res <- mt.rawp2adjp(rpraw, procs) # from multtest
## adjp <- res$adjp[order(res$index), ]
adjp <- cbind(rpraw, p.adjust(rpraw, "BH"),p.adjust(rpraw,"BY"))
# TODO: TV use names Bonferroni Holm Hochberg SidakSS SidakSD BH
place.keep33 <- if (type == "BH"){
which(adjp[,2] <= FDR)
} else { # type == "BY"
which(adjp[,3] <= FDR)
}
sign.Probe.ID <- Probe.ID[place.keep33]
if (type == "BH") {
sign.genes <- data.frame(sign.Probe.ID,
place.keep33,
adjp[adjp[,2] <= FDR,1],
adjp[adjp[,2] <= FDR,2])
} else {
sign.genes <- data.frame(sign.Probe.ID,
place.keep33,
adjp[adjp[,3] <= FDR,1],
adjp[adjp[,3] <= FDR,3])
}
names(sign.genes) <- c("Probe.ID", "row.name", "raw p-values",
paste(type, "adjusted p values", sep = " "))
return(sign.genes)
}
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