bed2coverageMatrix.R

#!/usr/bin/env Rscript
suppressPackageStartupMessages(library("optparse"))

## parse command line arguments
option_list <- list(
	make_option(c("-i", "--bedFile"), help="input genomic coordinates in BED format (extension SHOULD be .bed)"),
	make_option(c("-b", "--bamFile"), help="input BAM file(s) (if multiple, seperate them by a comma)"),
	make_option(c("-w", "--windows"), help="number of windows used to divide the input coordinates (useful when computing coverage for gene body)"),
	make_option(c("-e", "--extend"), default=1000, help="number of base pairs by which to extend the coordinates (default: %default)"),
	make_option(c("-p", "--processors"), default=1, help="number of processors to use (default: %default)"),
    make_option(c("-v", "--coveragePlot"), action="store_true", help="make coverage plot as output"),
    make_option(c("-a", "--average"), action="store_true", help="instead of giving expression for each replicate, output only the mean (assumes that consecutive BAM files are replicates 1 and 2, respectively)")
)

parser <- OptionParser(usage = "%prog [options]", option_list=option_list)
opt <- parse_args(parser)

## check, if all required arguments are given
if(is.null(opt$bedFile) | is.null(opt$bamFile)) {
	cat("\nProgram: bed2coverageMatrix.R (R script to compute read coverage matrix for given genomic regions in BED format)\n")
	cat("Author: BRIC, University of Copenhagen, Denmark\n")
	cat("Version: 1.0\n")
	cat("Contact: pundhir@binf.ku.dk\n");
	print_help(parser)
	q()
}

## load libraries
suppressPackageStartupMessages(library(CoverageView))
suppressPackageStartupMessages(library(session))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(RColorBrewer))

####################
## For Debugging
#opt<-list()
#opt$bamFile <- "/home/pundhir/project/chip-seq-analysis/data_whale/histone_marks/mouse/h3k4me3_tall_jarid_wt_Rep1.bam,/home/pundhir/project/chip-seq-analysis/data_whale/histone_marks/mouse/h3k4me3_tall_jarid_wt_Rep2.bam,/home/pundhir/project/chip-seq-analysis/data_whale/histone_marks/mouse/h3k4me3_tall_jarid_ko_Rep1.bam,/home/pundhir/project/chip-seq-analysis/data_whale/histone_marks/mouse/h3k4me3_tall_jarid_ko_Rep2.bam"
#opt$matrixFile <- "matrix"
#opt$bedFile <- "test.bed"
#opt$extend <- 1000
#opt$processors <- 10
#opt$windows <- 100

bamFile <- unlist(strsplit(opt$bamFile, ","))

if(file.exists(sprintf("%s.session", opt$bedFile))) {
    coveragePlot <- opt$coveragePlot
    load(sprintf("%s.session", opt$bedFile))
    opt$coveragePlot <- coveragePlot
} else {
    cov.mat.list<-list()
    for(i in 1:length(bamFile)) {
        trm<-CoverageBamFile(bamFile[i])
        if(is.null(opt$windows)) {
            cov.mat <- cov.matrix(trm, coordfile=opt$bedFile, extend=as.numeric(opt$extend), num_cores=as.numeric(opt$processors), normalization="rpm")
        } else {
            cov.mat <- cov.matrix(trm, coordfile=opt$bedFile, no_windows=as.numeric(opt$windows), offset=as.numeric(opt$extend), num_cores=as.numeric(opt$processors), normalization="rpm")
        }
        cov.mat.list[[i]]<-cov.mat
    }
    #save.session(sprintf("%s.session", opt$bedFile))

    if(!is.null(opt$average)) {
        cov.mat.list.avg<-list()
        j <- 1
        for(i in seq(1, length(bamFile), 2)) {
            cov.mat.list.avg[[j]] <- (cov.mat.list[[i]]+cov.mat.list[[i+1]])/2
            j <- j+1
        }
        cov.mat.list<-cov.mat.list.avg
        names(cov.mat.list) <- unique(gsub("_Rep.*", "", basename(bamFile)))
    } else {
        names(cov.mat.list) <- basename(bamFile)
    }

    cov.mat.combined <- t(do.call(rbind, cov.mat.list))
}

write.table(cov.mat.combined, file = "", sep="\t", quote = F, col.names = T, row.names = T)

if(!is.null(opt$coveragePlot)) {
    draw.heatmap(data=cov.mat.list,outfile=sprintf("%s.png", opt$bedFile))
}

#save.session(sprintf("%s.session", opt$bedFile))

q()