geneBreakOverlap: Find overlaps between genomic features and breakpoints

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Find overlaps between genomic features and 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 two lists: geneBreaks, geneSamples

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.