Pos2Gene: Map sequencing variants to gene

In VPA: Variant Pattern Analyzer for next-generation sequencing study

Description

The function is used to annotate a variant to its gene. The annotation information is based on the refseq table downloaded from the UCSC genome browser.

Usage

Pos2Gene(chr, pos, level="gene", show.dist=FALSE, ref="hg19")

Arguments

chr	Chromosome name of the variant, such as 'chr1' or '1'.
pos	The location of variant in the Chromosome.
level	The annotation level for variants. It can be either "gene" (i.e., including intron region) or "exon" (i.e., without including intron region).
show.dist	Logical value. When a position is mapped as inter-gene, whether to show the distances from the two genes.
ref	The version of reference genome.

Value

A vector including gene annotation results.

Author(s)

Qiang Hu

See Also

getref

Examples

#Pos2Gene("1", "1000000", level="exon", show.dist=TRUE, ref="hg19")

VPA documentation built on May 2, 2019, 4:45 p.m.