DeROTS <- function(mtrx, grps, paired=FALSE, logged=TRUE, B=1000) {
require(DEGandMore);
require(ROTS);
prepared <- PrepareDe(mtrx, grps, paired);
mtrx <- prepared[[1]];
grps <- prepared[[2]];
paired <- prepared[[3]];
g <- c(rep(0, length(grps[[1]])), rep(1, length(grps[[2]])));
k <- min(nrow(mtrx)/2, min(5000, 1000*ceiling(ncol(mtrx)/50000*nrow(mtrx))));
res <- ROTS(mtrx, g, B=B, K=k, log=logged);
m1 <- rowMeans(mtrx[, grps[[1]], drop=FALSE]);
m2 <- rowMeans(mtrx[, grps[[2]], drop=FALSE]);
fc <- res$logfc;
pv <- res$pvalue;
qv <- res$FDR;
m1[is.na(m1)] <- 0;
m2[is.na(m2)] <- 0;
fc[is.na(fc)] <- 0;
pv[is.na(pv)] <- 1;
qv[is.na(qv)] <- 1;
s <- cbind(m1, m2, m2-m1, fc, pv, qv, res$d);
colnames(s) <- c(paste('Mean', names(grps), sep='_'), 'Mean_Change', 'LogFC', 'Pvalue', 'FDR', 'Stat_d');
rownames(s) <- rownames(mtrx);
list(stat=s, group=grps, rots=res[c('B', 'a1', 'a2', 'k', 'R', 'Z')]);
}
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