Nothing
findBoundCutoff <- function(xSet, method=c("normalNull","twoGaussiansNull"), mean.method="mode",
pvalue=FALSE, fdr=FALSE, pvalPlot=FALSE) {
stopifnot(inherits(xSet, "ExpressionSet"))
signal <- exprs(xSet)[,1]
if(method == "normalNull") {
pval <- normalNull(signal, mean.method = mean.method)
}
if(method == "twoGaussiansNull") {
pval <- twoGaussiansNull.BF(signal)
}
if(pvalPlot) {
hist(pval, breaks=1000, freq=FALSE, border="grey", main="Histogram of p",
xlab="pvalue")
}
if(pvalue) {
cut <- min(signal[pval <= pvalue], na.rm=TRUE)
}
if(fdr) {
adj.pval <- p.adjust(pval, method = "fdr")
cut <- min(signal[adj.pval <= fdr], na.rm=TRUE)
}
cutoff <- round(cut,2)
cat("Using bound.cutoff =", cutoff, "\n")
return(cutoff)
}
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