SRAdb (version 1.30.0)

IGVsession: Create an IGV session file

Description

This function will create an IGV session file

Usage

IGVsession(files, sessionFile, genome='hg18', VisibleAttribute='', destdir=getwd())

Arguments

files

Character vector of one or more filenames or urls to load - required.

sessionFile

String representing session file name - required

genome

String representing a genome that IGV knows about.

VisibleAttribute

Character vector of one or more IGV Visible Attributes to annotate data tracks to be loaded - optional.

destdir

Path where to save the IGV session file.

Value

An IGV session file with full file path.

Details

While the current state of an IGV session can be saved to a named session file that can be opened to restore the IGV session later on, a IGV session file can be manually or programmatically created to achieve more efficient data loading and better control of IGV. IGVsession function was developed to create such IGV session files. For details please check IGV web site: http://www.broadinstitute.org/igv/ControlIGV

See Also

IGVload, IGVgenome, IGVgoto

Examples

	library(SRAdb)
	exampleBams = file.path(system.file('extdata',package='SRAdb'),
	    dir(system.file('extdata',package='SRAdb'),pattern='bam$'))
	exampleSessionFile <- IGVsession(exampleBams, 'exampleBams.xml');
  	## Not run: 
#   	## Start IGV within R. You only need one IGV instance with listen port 60151 open.
#     startIGV()
# 	
# 	## Create a socket connection to IGV
# 	sock <- IGVsocket()
# 	## Wait until IGV fully launched and make sure the listen port for IGV is open (If not configured in IGV, follow these steops: IGV --> Perferences --> Advanced --> Check the checkbox 'Enable port' 60151.)
#   	IGVload(sock, exampleSessionFile)
#   	## End(Not run)