GRcoverageSummit-methods {compEpiTools} | R Documentation

## 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)

[Package compEpiTools version 1.14.1 Index]