DOQTL (version 1.8.0)

find.overlapping.genes: 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.

Value

Data.frame with gene locations and symbols.

Details

Gets the gene locations from MGI and variants.

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)