QC for brentlab RNAseq data

createIgvBatchscript

R Documentation

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

createIgvBatchscript(
  bam_list,
  granges,
  igv_genome,
  output_dir,
  output_file_basename,
  exit_browser = TRUE,
  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
`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