epivizr (version 1.4.6)

startStandalone: Start the standalone epiviz interface

Description

Create an epiviz session manager for the epiviz web application served from the localhost.

Usage

startStandalone(geneInfo = NULL, geneInfoName = "", seqinfo = NULL,  chr = NULL, start = NULL, end = NULL, start.args = list(), ...)

Arguments

geneInfo

An object containing gene annotation information. See register-methods for information on objects permitted.

geneInfoName

(character) The name of the gene annotation to display on the UI.

seqinfo

Seqinfo-class object containing sequence names and lengths. Ignored if geneInfo is not NULL.

chr

Sequence name to load the UI. If NULL, taken from seqinfo(geneInfo) or seqinfo in order.

start

Starting genomic position when loading UI. If NULL, taken from seqinfo(geneInfo) or seqinfo in order.

end

Ending genomic position when loading UI. If NULL, taken from seqinfo(geneInfo) or seqinfo in order.

start.args

List containing other arguments to pass startEpiviz.

...

Arguments passed to addDevice method of EpivizDeviceMgr when adding gene annotation. For instance, keepSeqlevels.

Value

An object of class EpivizDeviceMgr.

Details

One of geneInfo or seqinfo must be non-NULL. Otherwise an error is raised.

See Also

EpivizDeviceMgr-class register-methods

Examples

## Not run: 
# library(Mus.musculus)
# mgr <- startStandalone(Mus.musculus, geneInfoName="mm10",
#     keepSeqlevels=paste0("chr",c(1:19,"X","Y")))	
# ## End(Not run)