compEpiTools (version 1.6.3)

GRenrichment-methods: Determines the enrichment over a set of genomic regions given two BAM files

Description

Given a GRanges, and two BAM files, this method detetermines the coverage of the 1st BAM file (bam) and of the 2nd BAM file (bamRef), both normalized by millions of reads in the library. Subsequently, the enrichment is computed as log2(bam - bamRef).

Methods

To be used in this form: GRenrichment(Object, bam, bamRef) where:

• Object: a GRanges
• bam: path to a BAM file
• bamRef: path to a BAM file, to be used as reference This is typically useful when applied to BAM files derived from ChIP-seq experiments, where bam and bamRef are the result of the alignment of ChIP and input reads, respectively.

An array of length equal to the length of Object is returned, containing the enrichment values. The enrichment of a given genomic region in Object is set to NA if in either bam or bamRef there are no reads, while it is -Inf of the same normalized coverage is found for both bam and bamRef (as in the example). The bam file has to be associated to the corresponding index .bai file. Please refer to the documentation of samtools on how to create it.

Examples

bampath <- system.file("extdata", "ex1.bam", package="Rsamtools")
gr <- GRanges(seqnames=Rle(c('seq1','seq2')), 
	ranges=IRanges(start=c(1000, 100), end=c(2000, 1000)))
 # bam and bamRef should not be pointing to the same file in real life ..
GRenrichment(Object=gr, bam=bampath, bamRef=bampath)