# bridge
# http://bioconductor.org/packages/3.3/bioc/html/bridge.html
# DeBridge
DeBridge <- function(mtrx, grps, paired=FALSE, logged=TRUE, ...) {
require(DEGandMore);
require(bridge);
prepared <- PrepareDe(mtrx, grps, paired);
mtrx <- prepared[[1]];
grps <- prepared[[2]];
paired <- prepared[[3]];
if (paired) warning("Paired test not supported by this method; performing unpaired test instead.\n");
d1 <- mtrx[, grps[[1]], drop=FALSE];
d2 <- mtrx[, grps[[2]], drop=FALSE];
res <- bridge.2samples(d1, d2, log=logged, all.out=FALSE, robust = FALSE, B=5000);
pv <- pmax(0, 1-res$post.p);
qv <- p.adjust(pv, method='BH');
m1 <- rowMeans(d1, na.rm=TRUE);
m2 <- rowMeans(d2, na.rm=TRUE);
if (logged) l2 <- m2-m1 else {
mn <- min(mtrx[mtrx>0]);
l2 <- log2(pmax(mn, m2)) - log2(pmax(mn, m1));
};
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, bridge=res);
}
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