compEpiTools (version 1.6.3)

GRcoverageSummit-methods: Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range

Description

Based on a GRanges and a BAM file (and optionally a control BAM file), returns a GRanges with the positions of maximum coverage within each range; it can be used to identify peak summits in ChIPseq enriched regions.

Methods

To be used in this form: GRcoverageSummit(Object, bam, bamControl=NULL) where:

• Object: GRanges
• bam: a BAM file path
• bamControl: a BAM file path

The method returns a GRanges with regions of width 1 pointing to the position of higher coverage. If the optional bamControl is provided, typically the ChIP-seq input sample, the bamControl coverage is subtracted from the bam coverage before identifying the maximum. If multiple maxima exist in a range, one is returned at random. 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)))
GRcoverageSummit(Object=gr, bam=bampath)