makeBranchpointWindowForSNP: Makes a branchpointer formatted GRanges object from refsnp...
In betsig/branchpointer: Prediction of intronic splicing branchpoints

Description Usage Arguments Value Author(s) Examples

View source: R/makeBranchpointWindowForSNP.R

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

1 2	makeBranchpointWindowForSNP(refSNP, mart.snp, exons, maxDist = 50, filter = TRUE)

`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?

formatted SNP query GRanges

Beth Signal

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)