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

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

create IGV viewer batch script (single range, as many tracks as you like)

Description

this will create a batch script that may be run with the igv browser. An example command is given in the examples below. See the extern data for an example of what one of these scripts looks like.

Usage

igv_script(
  x,
  locus,
  output_dir = getwd(),
  image_basename = "",
  exit_browser = TRUE,
  maxPanelHeight = 500,
  ...
)

Arguments

locus	the locus you wish to visualize. This will be used to filter the granges attribute of the object
output_dir	directory to which igv snapshot images will be deposited by igv
image_basename	basename of the igv snapshot files, eg ckf44_12345_run2. The output_dir and additional locus details, etc will be appended to this
exit_browser	Default is TRUE, which means that the batchscript will be written in a way that the browser will take an image, save it, and exit. Set to false and this script may be used to launch an interactive session.
maxPanelHeight	default 500. height of the IGV window
bam_list	list of bamfiles – multiple files means multiple tracks

Value

None. This prints a batch script to the output dir

Note

run on the command line like so xvfb-run –auto-servernum igv.sh -b script.bat

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.