output_index <- "" resultsList <- list() i <- 0 methodN <- c() dofabia <- TRUE dobeagle <- TRUE doplink <- TRUE dogermline <- TRUE dodash <- TRUE dorelate <- FALSE domcmc <- FALSE resultsAll <- c() rowNN <- c() Headermax <- c("IBDtrueP","IBDfalseN","IBDfalseP","IBDtrueN","IBDsensitivity","IBDspecifity","IBDFDR","IBDFPR","IBDaccuracy","IBDF1","IBDMatthews", "IBDtruePSample","IBDfalseNSample","IBDfalsePSample","IBDtrueNSample","IBDsensitivitySample","IBDspecifitySample","IBDFDRSample","IBDFPRSample","IBDaccuracySample","IBDF1Sample","IBDMatthewsSample", "IBDtruePSnps","IBDfalseNSnps","IBDfalsePSnps","IBDtrueNSnps","IBDsensitivitySnps","IBDspecifitySnps","IBDFDRSnps","IBDFPRSnps","IBDaccuracySnps","IBDF1Snps","IBDMatthewsSnps") if (dofabia) { fabiaresM <- read.table(file= paste("fabiares",output_index,".txt",sep=""),skip=1) fabiaHeader <- c("runNumber","restarts","numberIBDs", "truePSample","falseNSample","falsePSample","trueNSample","sensitivitySample","specifitySample","FDRSample","FPRSample","accuracySample","F1Sample","MatthewsSample", "truePSnps","falseNSnps","falsePSnps","trueNSnps","sensitivitySnps","specifitySnps","FDRSnps","FPRSnps","accuracySnps","F1Snps","MatthewsSnps", "trueP","falseN","falseP","trueN","sensitivity","specifity","FDR","FPR","accuracy","F1","Matthews") colnames(fabiaresM) <- fabiaHeader fabiaMeans <- colMeans(fabiaresM) resultsAll <- rbind(resultsAll,fabiaMeans[(-1:-3)]) rowNN <- c(rowNN,"FABIA") } beagleHeader <- c("runNumber", "truePSample","falseNSample","falsePSample","trueNSample","sensitivitySample","specifitySample","FDRSample","FPRSample","accuracySample","F1Sample","MatthewsSample", "truePSnps","falseNSnps","falsePSnps","trueNSnps","sensitivitySnps","specifitySnps","FDRSnps","FPRSnps","accuracySnps","F1Snps","MatthewsSnps", "trueP","falseN","falseP","trueN","sensitivity","specifity","FDR","FPR","accuracy","F1","Matthews") if (dobeagle) { beagleres1M <- read.table(file=paste("beagleres1",output_index,".txt",sep=""),skip=1) colnames(beagleres1M) <- beagleHeader beagleres2M <- read.table(file=paste("beagleres2",output_index,".txt",sep=""),skip=1) colnames(beagleres2M) <- beagleHeader beagle1Means <- colMeans(beagleres1M) beagle2Means <- colMeans(beagleres2M) resultsAll <- rbind(resultsAll,beagle1Means[-1],beagle2Means[-1]) rowNN <- c(rowNN,"BEAGLE 1","BEAGLE 2") } if (doplink) { plinkresM <- read.table(file=paste("plinkres",output_index,".txt",sep=""),skip=1) plinkHeader <- beagleHeader colnames(plinkresM) <- plinkHeader plinkMeans <- colMeans(plinkresM) resultsAll <- rbind(resultsAll,plinkMeans[-1]) rowNN <- c(rowNN,"PLINK") } if (dogermline) { germlineres1M <- read.table(file=paste("germlineres1",output_index,".txt",sep=""),skip=1) germlineHeader <- beagleHeader colnames(germlineres1M) <- germlineHeader germlineres2M <- read.table(file=paste("germlineres2",output_index,".txt",sep=""),skip=1) colnames(germlineres2M) <- germlineHeader germline1Means <- colMeans(germlineres1M) germline2Means <- colMeans(germlineres2M) resultsAll <- rbind(resultsAll,germline1Means[-1],germline2Means[-1]) rowNN <- c(rowNN,"GERMLINE 1","GERMLINE 2") } if (dodash) { dashresM <- read.table(file= paste("dashres",output_index,".txt",sep=""),skip=1) dashHeader <- c("runNumber","numberClusters", "truePSample","falseNSample","falsePSample","trueNSample","sensitivitySample","specifitySample","FDRSample","FPRSample","accuracySample","F1Sample","MatthewsSample", "truePSnps","falseNSnps","falsePSnps","trueNSnps","sensitivitySnps","specifitySnps","FDRSnps","FPRSnps","accuracySnps","F1Snps","MatthewsSnps", "trueP","falseN","falseP","trueN","sensitivity","specifity","FDR","FPR","accuracy","F1","Matthews") colnames(dashresM) <- dashHeader dashMeans <- colMeans(dashresM) resultsAll <- rbind(resultsAll,dashMeans[(-1:-2)]) rowNN <- c(rowNN,"DASH") } #relateresM <- read.table(file="relateres.txt",skip=1) #mcmcresM <- read.table(file="mcmcres.txt",skip=1) rownames(resultsAll) <- rowNN write.table(resultsAll,file= paste("resultsAll",output_index,".txt",sep=""),sep="\t")