buildAnnotationTracks: Build annotation tracks for visualizing using Gviz package

Description

Build annotation tracks for visualizing using Gviz package

Usage

buildAnnotationTracks(gene, extendRange = c(2000, 2000), includeGeneBody = TRUE, cytobandInfo = NULL, CpGInfo = NULL, genomeAxis = TRUE,  lib = "org.Hs.eg.db", genome = "hg19", genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", selectTranscripts=NULL,...)

Arguments

gene

An Entrez gene id or a GRanges object with length equals one

extendRange

extended range on each side of the gene

includeGeneBody

whether to include genebody of the provided gene

cytobandInfo

cytoband information. Set NA to suppress it.

CpGInfo

CpG-island information, GRanges or bed file are supported

genomeAxis

whether to add genome axis or not

lib

gene annotation library

genome

genome version

genomicFeature

genomic features: "TxDb" library or object, "Mart" object

selectTranscripts

selected transcripts to show in the annotation track. If it is NULL, all transcripts will be shown.

...

other parameters used by createTranscriptTrack function

Value

A list of different annotation Tracks

Details

This function aims to build annotation tracks to be visualized using Gviz package. If the cytobandInfo and CpGInfo are NULL and internet connection is available, it will download information directly from UCSC website. Set them as NAs if you want suppress this default behavior.

Examples

Run this code

if (require(TxDb.Hsapiens.UCSC.hg19.knownGene) && require(Gviz)) {
	annotationTracks <- buildAnnotationTracks('1826', includeGeneBody = FALSE, genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene")
}