R/fcrosTtest.R

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

fcrosTtest <-
function(xdata, cont, test, log2.opt = 0) {
    n <- nrow(xdata);
    idnames <- rownames(xdata);
    xcol <- colnames(xdata);
    n.xcol <- length(xcol);
    idx1 <- xcol %in% cont;
    m1 <- sum(idx1 == TRUE);
    idx2 <- xcol %in% test;
    m2 <- sum(idx2 == TRUE);
    m <- m1+m2;

    # form ttest data matrix
    dmat <- matrix(c(rep(0,n*m)), ncol = m);
    if (log2.opt) {
       x1 <- log2(xdata[, idx1 == TRUE]);
    } else {
       x1 <- xdata[,idx1 == TRUE];
    }
    dmat[,1:m1] <- as.matrix(x1);
    if (log2.opt) {
       x2 <- log2(xdata[,idx2 == TRUE]);
    } else {
       x2 <- xdata[,idx2 == TRUE];
    }
    dmat[,(m1+1):m] <- as.matrix(x2);

    FC <- matrix(c(rep(0,n)), ncol = 1);
    p.value <- matrix(c(rep(0,n)), ncol = 1);
    stat <- matrix(c(rep(0,n)), ncol = 1);
    # compute fold changes and p-values
    for (i in 1:n) {
        x1 <- dmat[i,1:m1];
        x2 <- dmat[i,(m1+1):m];
        if ((sd(x1)+sd(x2)) == 0.0) {
           p.value[i] <- 1.0;
           stat[i] <- 0.0;
        } else {
               tt <- t.test(x1,x2,var.equal = TRUE);
               p.value[i] <- tt$p.value;
               stat[i] <- tt$statistic;
        }
        FC[i] <- mean(2^x2)/mean(2^x1);
    }
     list(idnames=idnames, FC = FC, p.value = p.value, stat = stat);
}