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