getRegionOL: Returns overlapping named ranges for input ranges

Description Usage Arguments Details Value Examples

View source: R/getRegionOL.R

Description

Returns overlapping named ranges for input ranges

Usage

1
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

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