AutoIGV: Function to produce IGV session files and screenshorts...
In mumichae/DASSIE: Detection of Alternative Transcription Start Sites

Description Usage Arguments Value Author(s)

Function to produce IGV session files and screenshorts automatically

AutoIGV(
  coords,
  indents = c(0, 0),
  bams.paths,
  refs.paths = data.table(paths = ""[0], name = ""[0]),
  max.matrix = data.table(),
  folder.name = tempdir()
)

`coords`	data frame with 6 columns: chr, start, end, maximum, coverage.only and suffix.to.file. Maximum is the maximum of the coverage tracks to be displayd. If you want to use auto maximum, put -1 to maximum column. Column coverage.only indicates, whatever or not only coverage tracks should be displayed: FALSE, if you want reads to be displayed too and TRUE otherwise. Column suffix.to.file contains suffixes to be appended to files names
`indents`	vector of the nuumber of nucleoteds to be dysplayed from the left and rigth of region of interest. Default value is c(0, 0)
`bams.paths`	vector, containing paths to bam files. The order matters: tracks will appear in igv according to the order of this vector
`refs.paths`	vector, containing paths to reference files. The order also matters
`folder.name`	name of the folder to put results in
`coverage.only`	boolean, indicating, whatever or not only coverage tracks will be diplayed