R/wmw.R

In statTarget: Statistical Analysis of Molecular Profiles

### Wilcoxon-Mann Whitney tests This function provide two.sided Wilcoxon Mann Whitney tests for each
### pairwise comparison of sample groups.  file The connection to the data file.  wmw(file) A matrix
### with p values
wmw <- function(file) {
    pwdfile = paste(getwd(), "/Univariate/DataTable.csv", sep = "")
    file = pwdfile
    x <- read.csv(file, sep = ",", header = TRUE)
    x.x = x[, 3:ncol(x)]
    rownames(x.x) = x[, 2]
    k = matrix(x[, 1], ncol = 1)
    slink = paste(getwd(), "/DataPretreatment", "/slink.csv", sep = "")
    slink = read.csv(slink, header = TRUE)
    x.n = cbind(k, x.x)
    sorted = x.n[order(x.n[, 1]), ]
    g = c()
    for (i in 1:nrow(sorted)) {
        if (any(g == sorted[i, 1])) {
            g = g
        } else {
            g = matrix(c(g, sorted[i, 1]), ncol = 1)
        }
    }
    NoF = nrow(g)
    dirout.wm = paste(getwd(), "/Univariate/MannWhitneyTests/", sep = "")
    dir.create(dirout.wm)
    for (i in 1:NoF) {
        for (j in 1:NoF) {
            if (i < j) {
                ni = paste("r.", ExcName(i, slink), ".csv", sep = "")
                nj = paste("r.", ExcName(j, slink), ".csv", sep = "")
                pwdi = paste(getwd(), "/Univariate/Groups/", ni, sep = "")
                pwdj = paste(getwd(), "/Univariate/Groups/", nj, sep = "")
                I = read.csv(pwdi, header = TRUE)
                J = read.csv(pwdj, header = TRUE)
                I = I[, -1]
                J = J[, -1]
                fin = ncol(sorted) - 1
                # perform WMW test for the effective combinations and extract p-values
                wilx.pv <- matrix(rep(NA, fin))
                for (q in 1:fin) {
                  wilx.pv[q, ] <- wilcox.test(I[, q], J[, q], paired = FALSE, exact = NULL, correct = FALSE, 
                    conf.level = 0.95, alternative = "two.sided")$p.value
                }
                rownames(wilx.pv) <- colnames(x.x)
                colnames(wilx.pv) <- c("pvalue")
                
                wmw.ij.pv = paste("WMWTest_pvalues_", ExcName(i, slink), "vs", ExcName(j, slink), 
                  ".csv", sep = "")
                assign(wmw.ij.pv, wilx.pv)
                write.csv(wilx.pv, paste(dirout.wm, wmw.ij.pv, sep = ""))
            }
        }
    }
}