buildAnnotationTracks: Build annotation tracks for visualizing using Gviz package
In methyAnalysis: DNA methylation data analysis and visualization

Description Usage Arguments Details Value Author(s) See Also Examples

Build annotation tracks for visualizing using Gviz package

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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,...)

`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

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.

A list of different annotation Tracks

Pan Du

help

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