DeDexus <- function(mtrx, grps, paired=FALSE, norm='RLE') {
require(DEGandMore);
require(dexus);
prepared <- PrepareDe(mtrx, grps, paired);
mtrx <- prepared[[1]];
grps <- prepared[[2]];
paired <- prepared[[3]];
if (paired) warning("Paired test not supported by dexus; performing unpaired test instead.\n");
n <- sapply(grps, length);
l <- as.factor(rep(names(grps), sapply(grps, length)));
###########################################################################
res <- dexus(mtrx, label = l, normalization = norm, resultObject = 'list');
###########################################################################
pv <- res$pval;
qv <- p.adjust(pv, method='BH');
l2 <- res$logfc[, 2]/log(2);
m1 <- res$means[, 1];
m2 <- res$means[, 2];
m1[is.na(m1)] <- 0;
m2[is.na(m2)] <- 0;
l2[is.na(l2)] <- 0;
pv[is.na(pv)] <- 1;
qv[is.na(qv)] <- 1;
s <- cbind(m1, m2, m2-m1, l2, pv, qv);
colnames(s) <- c(paste('Mean', names(grps), sep='_'), 'Mean_Change', 'LogFC', 'Pvalue', 'FDR');
rownames(s) <- rownames(mtrx);
list(stat=s, group=grps, dexus=res);
}
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