find.overlapping.genes {DOQTL} | R Documentation

## find.overlapping.genes

### Description

FALSEind genes that intersect with a given set of variants.

### Usage

      find.overlapping.genes(variants,
      mgi.file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz",
      type = c("gene", "exon"))

### Arguments

`variants` | Data.frame with variants. The type attribute must be set to one of "snp", "indel", or "sv".
`mgi.file` | Character. FALSEull path to the MGI gene file. Defaults to "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz"
`type` | Character. One of "gene" or "exon". Indicates whether to intersect SNPs with genes (from beginning to end, including introns) or exons only.

### Details

Gets the gene locations from MGI and variants.

### Value

Data.frame with gene locations and symbols.

### Author(s)

Daniel Gatti

### See Also

`get.mgi.features{get.mgi.features}`

### Examples

      ## Not run:
        data(example.snps)
        x = find.overlapping.genes(variants = example.snps[19478:19506,])

    ## End(Not run)

[Package DOQTL version 1.16.2 Index]