categorize.variants: categorize.variants

In SNPtools: Accessing, subsetting and plotting mouse SNPs.

Description

This function intersects the given variants with the genes in that region and classifies them according to "intergenic", "3UTR", "exon", "intron" or "5UTR".

Usage

 categorize.variants(variants, 
        mgi.file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz") 

Arguments

variants	data.frame, Variants as returned by get.variants{get.variants}.
mgi.file	Character, full path to the MGI feature file. On the JAX campus, this defaults to "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz".

Value

For SNPs and Indels: data.frame: with eight columns: ID, CHR, POS, REF, ALT, symbol, id, type. The first four columns are simply copied over from the SNP file. The symbol column contains the Gene Symbol. The id column contains a gene ID (MGI, Ensembl, NCBI or VEGA). The type column contains "intergenic", "3UTR", "exon", "intron" or "5UTR", depending on the location of the variant in a gene.

For SVs: data.frame: with eight columns: ID, CHR, POS, REF, ALT, symbol, id, type. The first four columns are simply copied over from the SNP file. The symbol column contains the Gene Symbol. The id column contains a gene ID (MGI, Ensembl, NCBI or VEGA). The type column contains "intergenic", "3UTR", "exon", "intron" or "5UTR", depending on the location of the variant in a gene.

Author(s)

Daniel Gatti

See Also

get.variants{get.variants}

Examples

  data(example.snps)
  snp.type = categorize.variants(variants = example.snps[1:50,])

SNPtools documentation built on May 29, 2017, 3:12 p.m.