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

In betsig/branchpointer: Prediction of intronic splicing branchpoints

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

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