geneBreakOverlap: Find overlaps between genomic features and SV breakpoints;

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Find overlaps between genomic features and SV breakpoints;

Usage

geneBreakOverlap(ggr, svgr)

Arguments

ggr	(S4) a GenomicRanges object containing gene annotations. It is crutial that the genome version 'genesgr' and the input 'sv' are the same. The GRanges object must contain 'strand' and a metadata field 'gene_id' with unique values. Seqnames are expected in the format (chr1, chr2, ...).
svgr	(S4) a GenomicRanges object containing SV breakpoint ends. Metadata must contain 'rowid' and 'sampleid' fields. Seqnames are expected in the format (chr1, chr2, ...). Used by 'svc.break.annot' and 'cnv.break.annot'

Value

a list containing teo lists: geneBreaks, geneSamples

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.