#####define segments, overlap, filename ####### shiftSize <- 5000 segmentSize <- 10000 fileName="ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes" # without type #####compute how many segments we have####### ina <- as.numeric(readLines(paste(fileName,"_mat.txt",sep=""),n=2)) snps <- ina[2] over <- segmentSize%/%shiftSize N1 <- snps%/%shiftSize endRunA <- (N1-over+2) startRun=1 endRun=640 prefixPath="" sparseMatrixPostfix="_mat" annotPostfix="_annot.txt" samplesPostfix="_samples.txt" samples=0 #snps and samplesN load(file=paste(fileName,"_All",".Rda",sep="")) #indi load(file="individuals.Rda") for (posAll in startRun:endRun) { start <- (posAll-1)*shiftSize end <- start + segmentSize if (end > snps) { end <- snps } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste(fileName,pRange,"_resAnno.Rda",sep="")) mergedIBD <- resHapFabia$mergedIBD noIBD <- length(mergedIBD) if (noIBD>0) { for (ibdC in 1:noIBD) { noSample <- mergedIBD[[ibdC]]$noSamples labelsEUA <- indi[noSample,2] labelsNAA <- indi[noSample,1] labelsTechA <- indi[noSample,4] labels_ALLA <- paste(labelsNAA,labelsEUA,sep="_") mergedIBD[[ibdC]]$countrySamples <- labelsEUA mergedIBD[[ibdC]]$idSamples <- labelsNAA mergedIBD[[ibdC]]$labelSamples <- labels_ALLA mergedIBD[[ibdC]]$techSamples <- labelsTechA } } resHapFabia$mergedIBD <- mergedIBD ibd2excel(resHapFabia$mergedIBD,paste(fileName,pRange,".csv",sep="")) save(resHapFabia,annot,file=paste(fileName,pRange,"_resAnno",".Rda",sep="")) load(file=paste(fileName,pRange,"_resIBD.Rda",sep="")) noIBD <- length(mergedIBD) if (noIBD>0) { for (ibdC in 1:noIBD) { noSample <- mergedIBD[[ibdC]]$noSamples labelsEUA <- indi[noSample,2] labelsNAA <- indi[noSample,1] labelsTechA <- indi[noSample,4] labels_ALLA <- paste(labelsNAA,labelsEUA,sep="_") mergedIBD[[ibdC]]$countrySamples <- labelsEUA mergedIBD[[ibdC]]$idSamples <- labelsNAA mergedIBD[[ibdC]]$labelSamples <- labels_ALLA mergedIBD[[ibdC]]$techSamples <- labelsTechA } } save(mergedIBD,res,sPF,annot,resIBD1,resIBD2,mergedIBD1,mergedIBD2,file=paste(fileName,pRange,"_resIBD.Rda",sep="")) }