inst/eval/GSE29172/06.pAUCtable.R

In mpierrejean/jointSeg-1: Joint Segmentation of Multivariate (Copy Number) Signals

## Generation of xtable for Briefings in Bioinformatics.
dataSet <- "GSE29172,ASCRMAv2,H1395vsBL1395"
methTags <- c(sprintf("RBS+DP:log(c),d (Kmax=%s)", candK),
              sprintf("GFLars+DP:log(c),d (Kmax=%s)", candK),
              "PSCBS",
              sprintf("RBS+DP:log(c) (Kmax=%s)", candK),
              sprintf("GFLars+DP:log(c) (Kmax=%s)", candK),
              "CBS:log(c)",
              sprintf("DP:log(c) (Kmax=%s)", candK),
              sprintf("RBS+DP:d (Kmax=%s)", candK),
              sprintf("GFLars+DP:d (Kmax=%s)", candK),
              "CBS:d",
              sprintf("DP:d (Kmax=%s)", candK)
              )

tol <- 5;
aucMeth <- sapply(methTags, function(methTag){
  aucContamination <- NULL
  aucContaminationMom <- NULL
  for(pp in pct){
    simTag <- sprintf("ROC,n=%s,K=%s,regSize=%s,minL=%s,pct=%s", len, K, regSize, minL, pp)
    simName <- sprintf("%s,%s", dataSet, simTag)
    AucPath <- "aucData"
    fpath <- file.path(AucPath, simName)
    fpath <- Arguments$getWritablePath(fpath)
    filename <- sprintf("%s,B=%s,%s,aucData,relax=%s.xdr", simName, B, methTag, relax)
    pathname <- file.path(fpath, filename)
    if(file.exists(pathname)){
        auc <- loadObject(pathname)
        indtol <- which(tols==tol)
        aucContamination <- c(aucContamination, auc[indtol, "meanAUC"])
        aucContaminationMom <- c(aucContaminationMom, auc[indtol, "masOmenoAUC"])
    }else{
        aucContamination <- c(aucContamination, NA)
        aucContaminationMom <- c(aucContaminationMom,NA)
    }
}
  return(aucContamination)
})
rownames(aucMeth) <- sprintf("%s", pct)
colnames(aucMeth) <- methTags <-  c("PSCBS", "GFLars", "RBS", "CBS", "GFLars", "RBS", "cghseg", "CBS", "GFLars", "RBS", "cghseg")

order2D <- apply(t(aucMeth)[1:3, ], 2, function(cc){order(cc, decreasing=TRUE)})[1, ]
orderCn <- apply(t(aucMeth)[4:7, ], 2, function(cc){order(cc, decreasing=TRUE)})[1, ]
orderBaf <- apply(t(aucMeth)[8:11, ], 2, function(cc){order(cc, decreasing=TRUE)})[1, ]

methBaf <- c("CBS:d|het",
             sprintf("GFLars+DP:d|het (Kmax=%s)", candK),
             sprintf("RBS+DP:d|het (Kmax=%s)", candK),
             sprintf("cghseg:d|het (Kmax=%s)", candK)
             )[orderBaf]

methCn <-  c("CBS:log(c)",
             sprintf("GFLars+DP:log(c) (Kmax=%s)", candK),
             sprintf("RBS+DP:log(c) (Kmax=%s)", candK),
             sprintf("cghseg:log(c) (Kmax=%s)", candK)
             )[orderCn]

meth2D <-  c("PSCBS",
             sprintf("GFLars+DP:(log(c),d)|het (Kmax=%s)", candK),
             sprintf("RBS+DP:log(c),d|het (Kmax=%s)", candK)
             )[order2D]

matIndOrder <- apply(rbind(meth2D, methCn, methBaf), 2, function(cc){which(methTags%in%cc)})

matCond <- sapply(1:3, function(cc){t(aucMeth)[matIndOrder[, cc], cc]})
rownames(matCond) <- c("c,d", "c", "d")
colnames(matCond) <- sprintf("%s", pct)

library(xtable)
## Product latex table
xtable(t(aucMeth), align =c("l", "r", "r", "r"), caption=sprintf("Data Set 1: pAUC by method"))

xtable(matCond, align =c("l", "r", "r", "r"), caption=sprintf("pAUC By type  : Benchmark 1 :%s", dataSet))