snps.from.file: Import SNPs from a BED file or VCF file for use in motifbreakR

Description

Import SNPs from a BED file or VCF file for use in motifbreakR

Usage

snps.from.file(file = NULL, dbSNP = NULL, search.genome = NULL,
  format = "bed")

Arguments

file

Character; a character containing the path to a bed file or a vcf file see Details for a description of the required format

dbSNP

OPTIONAL; 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

format

Character; one of bed or vcf

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.file takes a character vector describing the file path to a bed file that contains the necissary information to generate the input for motifbreakR see http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1 for a complete description of the BED format. Our convention deviates in that there is a required format for the name field. name is defined as chromosome:start:REF:ALT or the rsid from dbSNP (if you've included the optional SNPlocs argument). For example if you were to include rs123 in it's alternate format it would be entered as chr7:24966446:C:A

Examples

Run this code

library(BSgenome.Drerio.UCSC.danRer7)
 library(SNPlocs.Hsapiens.dbSNP.20120608)
 snps.bed.file <- system.file("extdata", "danRer.bed", package = "motifbreakR")
 # see the contents
 read.table(snps.bed.file, header = FALSE)
 #import the BED file
 snps.mb <- snps.from.file(snps.bed.file,
                           search.genome = BSgenome.Drerio.UCSC.danRer7,
                           format = "bed")