snps.from.rsid {motifbreakR} | R Documentation

## 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

### Details

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

### 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.file` for an alternate method for generating a list of variants.

### Examples

    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)

[Package motifbreakR version 1.13.0 Index]