find.overlapping.genes: find.overlapping.genes

In SNPtools: Accessing, subsetting and plotting mouse SNPs.

Description

Find 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. Full 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)

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