makeBranchpointWindowForSNP {branchpointer} | R Documentation |
Searches Biomart for refsnp ids, and pulls genomic location and sequence identity information Reformats alleles so each query has only one alternative allele
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)