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

Description Usage Arguments Value Author(s)

View source: R/readQueryFile.R

Description

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

Usage

1
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


betsig/branchpointer documentation built on Sept. 27, 2021, 10:31 p.m.