makeGeneTrackAnnotation: Create a gene annotation object to use as gene track on the...
In epiviz/epivizr-release: R Interface to epiviz web app

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

Given an OrganismDb object, it creates a GRanges object in the required format to use with the epiviz UI. This allows users to create custom genome browsers from their Bioconductor environment.

1	makeGeneTrackAnnotation(object, kind = c("gene", "tx"), keepSeqlevels = NULL)

`object`	An object of class `OrganismDb`.
`kind`	return a "gene" or "transcript" annotation. Only gene annotations are currently supported.
`keepSeqlevels`	a list of seqnames to retain in the gene annotation. See `keepSeqlevels`

This function creates a GRanges object that can be used by the addDevice method in class EpivizDeviceMgr to add a genes track to an epiviz UI.

An object of class GRanges, with one row per gene. It includes columns Gene with gene symbol, and Exons including exon start and ends. The latter is of class IRangesList.

Hector Corrada Bravo

startStandalone

## Not run: 
library(Mus.musculus)
gr <- makeGeneTrackAnnotation(Mus.musculus, keepSeqlevels=paste0("chr", c(1:19, "X", "Y")))
mgr <- startEpiviz()
mgr$addSeqinfo(seqinfo(gr))
mgr$addDevice(gr, "mm10", type="geneInfo")

## End(Not run)