epivizr (version 1.4.6)

makeGeneTrackAnnotation: Create a gene annotation object to use as gene track on the epiviz UI.

Description

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.

Usage

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

Arguments

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

Value

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.

Details

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.

See Also

startStandalone

Examples

## 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)