snps.from.rsid: Import SNPs from rsid for use in motifbreakR

Description

Import SNPs from rsid for use in motifbreakR

Usage

snps.from.rsid(rsid = NULL, dbSNP = NULL, search.genome = NULL)

Arguments

rsid

Character; a character vector of rsid values from dbSNP

dbSNP

an object of class SNPlocs to lookup rsids; see availible.SNPs in injectSNPs to check for availible SNPlocs

search.genome

an object of class BSgenome for the species you are interrogating; see available.genomes for a list of species

Value

a GRanges object containing:
SNP_idThe rsid of the snp with the "rs" portion stripped
alleles_as_ambigTHE IUPAC ambiguity code between the reference and alternate allele for this SNP
REFThe reference allele for the SNP
ALTThe alternate allele for the SNP

Details

snps.from.rsid take an rsid, or character vector of rsids and generates the required object to input into motifbreakR

Examples

Run this code

library(BSgenome.Hsapiens.UCSC.hg19)
 library(SNPlocs.Hsapiens.dbSNP.20120608)
 snps.file <- system.file("extdata", "pca.enhancer.snps", package = "motifbreakR")
 snps <- as.character(read.table(snps.file)[,1])
 snps.mb <- snps.from.rsid(snps,
                           dbSNP = SNPlocs.Hsapiens.dbSNP.20120608,
                           search.genome = BSgenome.Hsapiens.UCSC.hg19)