Nothing
fcros2 <-
function(xdata1, xdata2, cont, test, log2.opt = 0, trim.opt = 0.25) {
idnames <- rownames(xdata1);
n1 <- nrow(xdata1);
n2 <- nrow(xdata2);
if (n1 != n2) stop('xdata1 and xdata2 should have the same number of rows');
n <- n1;
# compute FC matrix from dataset 1
fc1 <- fcrosFCmat(xdata1, cont, test, log2.opt, trim.opt);
m1 <- ncol(fc1$fcMat);
samp1 <- paste("V",as.character(1:m1), sep = "");
# compute FC matrix from dataset 2
fc2 <- fcrosFCmat(xdata2, cont, test, log2.opt, trim.opt);
m2 <- ncol(fc2$fcMat);
samp2 <- paste("W",as.character(1:m2), sep = "");
samp <- c(samp1, samp2);
m <- m1+m2;
idnames <- fc1$idnames;
fc <- matrix(c(fc1$fcMat, fc2$fcMat), ncol = m);
colnames(fc) <- c(samp);
rownames(fc) <- rownames(xdata1);
# compute the fold changes
FC <- 0.5*(fc1$FC + fc2$FC);
FC2 <- 0.5*(fc1$FC2+ fc2$FC2);
# perform analysis with fold changes matrix
af <- fcrosMod(fc, samp, log2.opt, trim.opt);
ri <- af$ri;
p.value <- af$p.value;
f.value <- af$f.value;
bounds <- af$bounds;
params <- af$params;
params_t <- af$params_t;
list(idnames=idnames, FC=FC, FC2=FC2, ri=ri, p.value=p.value,
f.value=f.value, bounds=bounds, params=params, params_t=params_t);
}
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