getRegionOL {netDx} | R Documentation

## Returns overlapping named ranges for input ranges

### 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)

[Package netDx version 1.0.3 Index]