readQueryFile: Read a query file

In betsig/branchpointer: Prediction of intronic splicing branchpoints

Description

Reads and formats a manually generated query file, and finds realtive locations of the closest annotated exons Converts unstranded SNPs to two entries for each strand. Checks for duplicate names and replaces if found.

Usage

readQueryFile(queryFile, queryType, exons, maxDist = 50, filter = TRUE)

Arguments

queryFile	tab delimited file containing query information. For intronic regions should be in the format: region id, chromosome name, region start, region end, strand. For SNP variants should be in the format: SNP id, chromosome name, SNP position, strand, reference allele (A/T/C/G), alternative allele (A/T/C/G)
queryType	type of query file ("SNP" or "region")
exons	GRanges containing exon co-ordinates. Should be produced by gtfToExons()
maxDist	maximum distance a SNP can be from an annotated 3' exon.
filter	remove SNP queries prior to finding finding nearest exons.

Value

Formatted query GRanges

Author(s)

Beth Signal

Examples

smallExons <- system.file("extdata","gencode.v26.annotation.small.gtf", package = "branchpointer")
exons <- gtfToExons(smallExons)

querySNPFile <- system.file("extdata","SNP_example.txt", package = "branchpointer")
querySNP <- readQueryFile(querySNPFile, queryType = "SNP", exons)

queryIntronFile <- system.file("extdata","intron_example.txt", package = "branchpointer")
queryIntron <- readQueryFile(queryIntronFile,queryType = "region", exons)

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