getHumanGenes: Get protein coding gene regions

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

getHumanGenes returns a GRanges object of all protein coding genes genome-wide or within specified chromosomes. Annotation is from regions from hg19/Gr37 and protein coding genes.

Usage

getHumanGenes(chr, cache = TRUE)

## S4 method for signature 'missing'
getHumanGenes(chr, cache = TRUE)

## S4 method for signature 'character'
getHumanGenes(chr, cache = TRUE)

Arguments

chr	A vector of chromosomes
cache	logic variable (default = TRUE) to use genes from July.2015 freeze

Details

This function returns a GRanges object with the coordinates and gene IDs of all protein coding genes either genome-wide (by default) orspecified within a particular chromosome.

Value

A GRanges object

Examples

# Grab all protein coding gene locations genome-wide
pc.genes <- getHumanGenes()
# Grab all protein coding gene loctions on chromosome 1
chr1 <- getHumanGenes(c('1'))

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.