Create Creat_Random_bins.R

Full Pipeline/Creat_Random_bins.R

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+# note, Create random bins (for a binSize) for one category (e.g. HumanFC), and then
+# copy that for others (e.g. EpiMap, CAGE, and TFs)
+
+library(dplyr)
+library(data.table)
+source = "HumanFC" 
+# ------------- Set Bin-flanking configuration
+binSize = 400
+flanking = 2*binSize # can be arbitrarily given
+dataDir = paste0("/Volumes/Data1/PROJECTS/DeepLearning/Test/", source, "/",binSize,"_",flanking,"/")
+# dataDir = paste0("/srv/scratch/z3526914/DeepBrain/Data/", source, "/",binSize,"_",flanking,"/")
+dir.create(dataDir, recursive=T)
+
+# ------------- Bin creation
+# set a fixed number of bins for this bin_flanking test:
+# Rationale: for smaller bin/flanking size, the number of bins will be huge
+# for which downstream data processing may suffer resource issue
+howManyBins = 1000000
+# chrSizeFileName = "/srv/scratch/z3526914/DeepBrain/Data/hg19.chrom.sizes.txt"
+chrSizeFileName = "/Volumes/Data1/PROJECTS/DeepLearning/Test/hg19.chrom.sizes.txt"
+chr_size = fread(chrSizeFileName, sep="\t") %>% as.data.frame()
+colnames(chr_size)=c("chr", "size")
+# remove chromosome patches and sort by chr number
+chr_size=chr_size[-grep("_", chr_size$chr, fixed=TRUE),]
+chr_size=chr_size[match(paste0("chr", c(c(1:22), "M", "X", "Y")), chr_size$chr), ]
+
+# 1. generate binIDs with size given, and chose randomly 1M of them: one File output
+# generate bed file of bins of size b
+message("Generating bed files for each bins of size b: ",appendLF=F)
+b=binSize
+for (j in c(1:nrow(chr_size))){
+ start=seq(from=0, to=chr_size$size[j], by=b)+1
+ end=seq(from=b, to=chr_size$size[j], by=b)
+ chr_bins=cbind(as.character(chr_size$chr[j]),start[1:length(end)],end)
+ if (j==1) bins=chr_bins else bins=rbind(bins, chr_bins) 
+}
+bins=as.data.frame(bins)
+colnames(bins)=c("chr", "start", "end")
+bins$id=paste(bins$chr, bins$start, bins$end, sep="_")
+# Note: no strand is mentioned, hence 1 less column in all the subsequent files
+
+binFile=paste0("hg19_bins_", b,"bp")
+fwrite(bins, file=paste0(dataDir,binFile,".bed"), sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE)
+message("Done",appendLF=T)
+# select randomly a fixed number of bins
+bin_inputFile = binFile
+bin_outputFile = paste0(bin_inputFile,"_rand")
+
+message(paste("Select", howManyBins, "bins randomly "),appendLF=F)
+system2('shuf', 
+ paste('-n', howManyBins, paste0(dataDir,bin_inputFile,".bed"), '>',paste0(dataDir,bin_outputFile,".bed"), sep=' '), 
+ wait=T)
+message("Done",appendLF=T)