categorize.variants {DOQTL}R Documentation

categorize.variants

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

FALSEor SNPs and Indels: data.frame: with eight columns: ID, CHR, POS, REFALSE, 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. FALSEor SVs: data.frame: with eight columns: ID, CHR, POS, REFALSE, 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}


[Package DOQTL version 1.16.2 Index]