methyAnalysis (version 1.14.0)

createTranscriptTrack: Create a transcript annotation track

Description

Create a transcript track, which is a GeneRegionTrack object

Usage

createTranscriptTrack(gene, genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", lib = "org.Hs.eg.db", 
	genome = "hg19", extendRange = c(2000, 2000), includeOtherGene=FALSE, includeGeneBody = TRUE, 
	thinBox_utrOnly = FALSE, background.title = "gray", fill = "#8282d2", ...)

Arguments

gene

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

genomicFeature

a TxDb library, TxDb object, or Mart object

lib

Entrez annotation library

genome

The version of genome

extendRange

extended range on each side of the gene

includeOtherGene

whether to include other genes in the same chromosome ranges, only useful when "gene" is a gene ID.

includeGeneBody

whether to include the whole gene body or not

thinBox_utrOnly

whether to only show UTRs as thin boxs in the plot

background.title

the background color of the title

fill

fill color for transcript track

...

other parameters

Value

a GeneRegionTrack object

Details

This function is to create a GeneRegionTrack object for visualization using Gviz package.

See Also

plotTracks, plotTracksWithDataTrackInfo, heatmapByChromosome, plotMethylationHeatmapByGene

Examples

if (require(TxDb.Hsapiens.UCSC.hg19.knownGene) && require(Gviz)) {
	rangeTrack <- createTranscriptTrack('7157', genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene")
	# plotTracks(rangeTrack)
}