getRegionOL: Returns overlapping named ranges for input ranges

In netDx: Network-based patient classifier

Description

Returns overlapping named ranges for input ranges

Usage

getRegionOL(gr, rngList)

Arguments

gr	(GRanges) query ranges
rngList	(list) keys are names, and values are GRanges, each range of which has a name (in 'name' column). Note: It is faster to provide a list of length 1 ; if the list is long, combining into a single GRanges object could prove slow.

Details

Given a set of query GRanges, and a subject list-of-GRanges, updates the query with a column 'LOCUS_NAMES' containing the names of ranges overlapped by the query. One application is to map structural variants, such as CNVs, to genes in pathways of interest. In this scenario gr would contain the patient CNVs, and rngList would be a list of GenomicRanges objects, one per cellular pathway.

Value

(GRanges) query ranges with the added column 'LOCUS_NAMES'. Where a range overlaps with multiple loci, the names are reported as a comma-separated vector

Examples

data(cnv_GR,pathway_GR)
x <- getRegionOL(cnv_GR,pathway_GR)

netDx documentation built on Dec. 11, 2020, 2:01 a.m.