makeBranchpointWindowForSNP: Makes a branchpointer formatted GRanges object from refsnp...

Description Usage Arguments Value Author(s) Examples

View source: R/makeBranchpointWindowForSNP.R

Description

Searches Biomart for refsnp ids, and pulls genomic location and sequence identity information Reformats alleles so each query has only one alternative allele

Usage

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makeBranchpointWindowForSNP(refSNP, mart.snp, exons, maxDist = 50,
  filter = TRUE)

Arguments

refSNP

Vector of refsnp ids

mart.snp

biomaRt mart object specifying the BioMart database and dataset to be used

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 SNP query GRanges

Author(s)

Beth Signal

Examples

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

mart.snp <- biomaRt::useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="www.ensembl.org")
query <- makeBranchpointWindowForSNP("rs587776767", mart.snp, exons)

branchpointer documentation built on Nov. 8, 2020, 6:16 p.m.