## 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))
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