phsc.cmd.process.phyloscanner.output.in.directory: Generate bash commands to process phyloscanner output

In olli0601/Phyloscanner.R.utilities:

Generate bash commands to process phyloscanner output

Description

This function generates bash commands that combine the various Rscripts in the phyloscanner toolkit

Usage

phsc.cmd.process.phyloscanner.output.in.directory(
  tmp.dir,
  file.patients,
  pty.args
)

Arguments

tmp.dir	Directory with phyloscanner output.
file.patients	File name of the file that contains the list of unique individuals/units that the bam files correspond to, possibly after re-naming.
pty.args	List of phyloscanner input variables.

Value

character string of bash commands.

olli0601/Phyloscanner.R.utilities documentation built on April 21, 2024, 1:59 p.m.