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f.QQconf <- function(nGenes=18, nSim=10000, quantiles=c(0.025, 0.975)) {
nSim <- nSim-1
## pmat <- matrix(NA, nrow=nSim, ncol=nGenes)
## for (i in 1:nSim) {
## pmat[i,] <- sort(-log(runif(nGenes), base=10))
## }
pmat <- matrix(-log(runif(nGenes*nSim), base=10), ncol=nGenes)
pmat <- apply(pmat, 1, sort)
nSim.first <- 10
pmat.first <- pmat[,1:nSim.first]
pmat.sort <- apply(pmat, 1, sort)
nq <- length(quantiles)
p.quant <- matrix(NA, nrow=nq, ncol=nGenes)
for (i in 1:nq) {
ind <- quantiles[i] * (nSim+1)
p.quant[i,] <- pmat.sort[ind,]
}
rownames(p.quant) <- quantiles
p.mean <- apply(pmat.sort, 2, mean)
## cat("p.mean=", p.mean, "\np.mean.true=", p.mean.true, "\n")
## p.lower <- pmat[]
list(first=pmat.first, mean=p.mean, quant=p.quant)
}
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