inst/eval/GSE11976/04.pAUC.R

In mpierrejean/jointSeg: Joint Segmentation of Multivariate (Copy Number) Signals

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## summarization of ROC curves : AUC cumputing
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ComputeAUC <- function(rocArray) {
    FPs <- 0:FPSup
    TPs <- sapply(FPs, FUN=function(FP) {
        apply(rocArray, 1, FUN=function(roc) {
            ww <- which(roc[, "FP"]<=FP)
            max(roc[ww, "TP"])
        })
    })
    TPs[is.infinite(TPs)] <- NaN
    denom <- sum(lintegrate(c(0, 0, FPSup), c(0, K, K), xint=c(0, 0, FPSup)))
    aucs <-  apply(TPs, 1, FUN=function(tp) {
        y <- c(0, tp)
        x <- c(0, FPs)
        sum(lintegrate(x, y, xint=x))
    })
    res <- aucs/denom
    res
}

for (mm in seq(along=methTags)) {
    print(methTags[mm])
    bestMatList <- NULL
    rocArrayList <- NULL
    rocArrayInitList <- NULL
    aucData <- NULL
    aucArray <- NULL
    methTag <- methTags[mm]
    for (tol in tols) {
        ## dyn prog path
        filename <- sprintf("%s,B=%s,%s,rocArray,tol=%s,relax=%s.xdr", simNameNF, B, methTag, tol, relax)
        pathname <- file.path(epath, filename)
        print(file.exists(pathname))
        if(file.exists(pathname)){
            rocArray <- loadObject(file=pathname)## RocArray for tol and methTag
            aggFUN <- eval(as.name(sprintf("ComputeAUC")))
            auc <- aggFUN(rocArray)
            ## roc curves
            masomeno <-  2*sd(auc)/sqrt(B)
            aucMean <- mean(auc)
            aucData <- rbind(aucData,c(aucMean, masomeno))
            aucArray <- rbind(aucArray,auc)
        }
    }## End tol
    AucPath <- "aucData"
    fpath <- file.path(AucPath, simName)
    fpath <- Arguments$getWritablePath(fpath)
    filename <- sprintf("%s,B=%s,%s,aucArray,relax=%s.xdr", simNameNF, B, methTag, relax)
    pathname <- file.path(fpath, filename)
    if(!is.null(aucArray)){
        saveObject(aucArray, pathname)
    }
    fpath <- file.path(AucPath, simName)
    fpath <- Arguments$getWritablePath(fpath)
    filename <- sprintf("%s,B=%s,%s,aucData,relax=%s.xdr", simNameNF, B, methTag, relax)
    pathname <- file.path(fpath, filename)
    if(!is.null(aucData)){
        dimnames(aucData) <- list(NULL, c("meanAUC", "masOmenoAUC"))
        saveObject(aucData, pathname)
    }
    ## aucData contains for method methTag, a table with mean of Auc for various tolerance
}