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]