Nothing
calcSRmatMod <- function(xdata, samp, log2.opt=0, trim.opt=0.25) {
n <- nrow(xdata);
xcol <- colnames(xdata);
n.xcol <- length(xcol);
idx <- xcol %in% samp;
m <- sum(idx);
# form data matrix
fmat <- matrix(c(rep(0,n*m)), ncol = m);
if (log2.opt) {
x1 <- log2(xdata[, idx]);
} else {
x1 <- xdata[, idx];
}
fmat <- as.matrix(x1);
# compute matrix containing pairwise fold changes
rvectC <- c(fmat[, 1:m]);
rmat <- apply(fmat, 2, rank, ties.method = "average")/n;
# if (trim.opt), reduce the standard rank matrix
if ((trim.opt > 0) & (trim.opt < 0.5)) {
deb <- round(trim.opt * m) + 1;
fin <- m - deb + 1;
idx <- deb:fin;
m2c <- length(idx);
rvect <- c(rmat[,1:m]);
rvect2 <- rmatTrim(rvect, n, m, idx, m2c);
rmat.sr <- matrix(rvect2, ncol = m2c);
rvect <- rvect2;
rmat.val <- moyStdCalc(rvect, n, m2c);
moyV <- rmat.val$moyC;
stdV <- rmat.val$stdC;
FC2 <- fc2Calc(rvectC, n, m, idx, m2c);
rm(rvect);
rm(rmat.val);
rm(rvectC);
}
else {
rmat.sr <- rmat;
m2c <- m;
idx <- 1:m2c;
rvect <- c(rmat.sr[,1:m2c]);
rmat.val <- moyStdCalc(rvect, n, m2c);
moyV <- rmat.val$moyC;
stdV <- rmat.val$stdC;
FC2 <- fc2Calc(rvectC, n, m, idx, m2c);
rm(rvect);
rm(rmat.val);
rm(rvectC);
}
list(rmat.sr=rmat.sr, moyV=moyV, stdV=stdV, FC2=FC2, m2c=m2c);
}
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