R/make.design.matrix.R

In maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

"make.design.matrix" <-
function (edesign, degree = 2, time.col = 1, repl.col = 2, group.cols = c(3:ncol(edesign))) 
{
    control.label <- colnames(edesign)[group.cols][1]
    if (dim(as.matrix(edesign))[2] > 3) {
        dummy.cols <- group.cols[2:length(group.cols)]
        treatm.label <- paste(colnames(edesign)[dummy.cols], 
            "vs", control.label, sep = "")
        groups.label <- c(control.label, treatm.label)
        matrix.dummy <- as.matrix(edesign[, dummy.cols])
        ## Shared origin
    dummy <- NULL
    j = 0
    origen  <- min(edesign[,time.col])
    origen <-edesign[edesign[,1]==origen,]
    for (i in 1:length(dummy.cols)) {
       share <- apply(origen[,c(3,dummy.cols[i])],1,sum)
       if  (!is.element(TRUE, share>1)) {
       j=j+1
          dummy <- cbind(dummy,matrix.dummy[,i])
          colnames(dummy)[j] <- treatm.label[i]
       } 
    }
        time <- as.matrix(edesign[, time.col])
        colnames(time) <- colnames(edesign)[time.col]
        dis <- cbind(dummy, time)
        rownames(dis) <- rownames(edesign)
        groups.vector <- c(colnames(dummy), control.label)
        colnames.dis <- colnames(dis)
        dis <- cbind(dis, dis[,ncol(dis)] * matrix.dummy)
        colnames(dis) <- c(colnames.dis, paste(colnames(edesign)[time.col], 
            "x", colnames(edesign)[dummy.cols], sep = ""))
        groups.vector <- c(groups.vector, treatm.label)
        if (degree >= 2) {
            for (i in 2:degree) {
                colnames.dis <- colnames(dis)
                dis <- cbind(dis, edesign[, time.col]^i, edesign[, 
                  time.col]^i * edesign[, dummy.cols])
                colnames(dis) <- c(colnames.dis, paste(colnames(edesign)[time.col], 
                  i, sep = ""), paste(colnames(edesign)[time.col], 
                  "", i, "x", colnames(edesign)[dummy.cols], 
                  sep = ""))
                groups.vector <- c(groups.vector, groups.label)
            }
        }
    }
    else {
        dis <- as.matrix(edesign[, time.col])
        colnames(dis) <- colnames(edesign)[time.col]
        rownames(dis) <- rownames(edesign)
        if (degree >1) {
           for (i in 2:degree) {
               colnames.dis <- colnames(dis)
               dis <- cbind(dis, edesign[, time.col]^i)
               colnames(dis) <- c(colnames.dis, paste(colnames(edesign)[time.col], 
                i, sep = ""))
           }
       }
        groups.vector <- rep(colnames(edesign)[group.cols], degree)
    }
    output <- list(dis, groups.vector, edesign)
    names(output) <- c("dis", "groups.vector", "edesign")
    output
}