getQueryLoc {branchpointer} | R Documentation

## Find the closest 3' and 5' exons to a branchpointer query

### Description

Finds the closest annotated exons from genomic co-ordinates in a branchpointer query GRanges

### Usage

    getQueryLoc(query, queryType, maxDist = 50, filter = TRUE, exons)

### Arguments

`query` | branchpointer query GenomicRanges must have chromosome at position 2, genomic co-ordinate at position 3, and strand at position 4.
`queryType` | type of query file (`"SNP"` or `"region"`)
`maxDist` | maximum distance a SNP can be from an annotated 3' exon.
`filter` | remove SNP queries prior to finding finding nearest exons.
`exons` | data.frame containing exon co-ordinates. Should be produced by gtfToExons()

### Value

GenomicRanges with the query and its location relative to the 3' and 5' exons

### Author(s)

Beth Signal

[Package branchpointer version 1.20.0 Index]