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 1.14.0 Index]