IGVsession: Create an IGV session file

In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

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.

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

Value

An IGV session file with full file path.

Author(s)

Jack Zhu <[e-mail]>

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)

zhujack/SRAdb documentation built on Oct. 26, 2022, 7:32 a.m.