createIgvBatchscript: create IGV viewer batch script (single range, as many tracks...

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

Description

this will create the following: new # batchscript keyword new (new snapshot) snapshotDirectory IGV_Snapshots # output directory maxPanelHeight 500 # maximum height of igv browser viewer genome organism.genome # igv .genome file load control.bam # load alignment files in bam_file_list load perturbed.bam goto chr1:1-100 # load region of interest snapshot batchfilename_locus1.png # saves a snapshot of the IGV window to an image file goto chr10:3-300 # repeat at another locus snapshot batchfilename_locus2.png exit # quit session

Usage

createIgvBatchscript(
  bam_list,
  granges,
  igv_genome,
  output_dir,
  output_file_basename,
  maxPanelHeight = 500
)

Arguments

bam_list	list of bamfiles – multiple files means multiple tracks
granges	granges describing the range you wish to visualize – range must be on one chromosome/contig
igv_genome	.genome file created by IGV tools
output_dir	where to deposit both the script and the browser shots
output_file_basename	this will serve as both the name of the browser shot after running IGV, and the name o the batchscript itself
maxPanelHeight	default 500. height of the IGV window

Value

None. This prints a batch script to the output dir

Examples

## Not run: 
# You need to have igv installed on the machine where you will run this. This
# is something you can run on your local. Create the browser shot like so:

xvfb-run --auto-servernum igv.sh -b script.bat


## End(Not run)

cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.