R/aucROC.R

In statTarget: Statistical Analysis of Molecular Profiles

### acu.ROC This function provide area under the Curve of ROC.  file The connection to the data in
### the Univariate file.  A matrix to outline the AUC.
aucROC <- 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.w = paste(getwd(), "/Univariate/ROC", sep = "")
    dir.create(dirout.w)
    
    for (i in 1:NoF) {
        for (j in 1:NoF) {
            
            if (i < j) {
                # pb <- txtProgressBar(min = 1, max = NoF, style = 3)
                
                # Sys.sleep(0.000001)
                
                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]
                Ilf = matrix(rep(1, i), nrow(I))
                Jlf = matrix(rep(0, j), nrow(J))
                colnames(Ilf) = c("lf")
                colnames(Jlf) = c("lf")
                I = cbind(Ilf, I)
                J = cbind(Jlf, J)
                IJ = rbind(I, J)
                IJM <- as.matrix(IJ[, 2:ncol(IJ)])
                outf <- as.factor(IJ[, 1])
                # message(paste('*Group.', ExcName(i,slink), sep = ''), ' Vs.', paste(' Group.', ExcName(j,slink),
                # sep = ''))
                myROC = function(x, y) {
                  roc.obj <- suppressMessages(ROC::rocdemo.sca(y, x, function(x, thresh) ROC::dxrule.sca(x, 
                    thresh)))
                  auc <- ROC::AUC(roc.obj)
                  # rocdata <- c(roc.obj$auc,auc.ci[1],auc.ci[3])
                  if (auc >= 0.5) {
                    return(auc)
                  } else {
                    return(1 - auc)
                  }
                }
                
                myroc <- apply(IJM, 2, function(x) {
                  myROC(x, outf)
                })
                
                # myroc <- apply(IJM,2,function(x){myROC(x,outf)})
                myroc <- as.data.frame(myroc)
                colnames(myroc) = c("AUC")
                
                myroc.ij = paste("auc_roc_", ExcName(i, slink), "vs", ExcName(j, slink), ".csv", sep = "")
                assign(myroc.ij, myroc)
                write.csv(myroc, paste(dirout.w, myroc.ij, sep = "/"))
                # setTxtProgressBar(pb, i)
                
                
            }
        }
    }
}