makeBranchpointWindowForSNP {branchpointer}R Documentation

Makes a branchpointer formatted GRanges object from refsnp ids

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

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

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)

[Package branchpointer version 1.18.0 Index]