snps.from.file {motifbreakR} | R Documentation

## 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",
      indels = FALSE
    )

### 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`

### 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

### Value

a GRanges object containing:

`SNP_id` | The rsid of the snp with the "rs" portion stripped
`alleles_as_ambig` | THE IUPAC ambiguity code between the reference and alternate allele for this SNP
`REF` | The reference allele for the SNP
`ALT` | The alternate allele for the SNP

### See Also

See `motifbreakR` for analysis; See `snps.from.rsid` for an alternate method for generating a list of variants.

### Examples

     library(BSgenome.Drerio.UCSC.danRer7)
     library(SNPlocs.Hsapiens.dbSNP142.GRCh37)
     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")

[Package motifbreakR version 2.8.0 Index]