# tweeDEseq
# http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html
# tweeDE {tweeDEseq}
DeTweeDeSeq <- function(mtrx, grps, paired=FALSE, cl=4, ...) {
require(DEGandMore);
require(tweeDEseq);
require(multicore);
prepared <- PrepareDe(mtrx, grps, paired);
mtrx <- prepared[[1]];
grps <- prepared[[2]];
paired <- prepared[[3]];
if (paired) warning("Paired test not supported by tweeDE; performing unpaired test instead.\n");
f <- rep(names(grps), sapply(grps, length));
ct <- normalizeCounts(mtrx);
res <- tweeDE(ct, group = f, mc.cores = max(1, cl));
pv <- res[, 6];
m1 <- res[, 2];
m2 <- res[, 3];
l2 <- res[, 4];
qv <- p.adjust(pv, method='BH');
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[rownames(mtrx), ], group=grps, tweeDEseq=res);
}
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