Wrapping BayPass

pyRona can take the output of BayPass as input to calculate the RONA values. Due to this, pyRona includes an R script named Baypass_workflow.R that can be used to automate and wrap BayPass analyses. Not that it is highly recommended that you read both BayPass's manual (and paper) a through read before using this script.

Baypass_workflow.R

This script will automate the workflow for the awesome BayPass software by M. Gautier, which is described in this paper. It does no error handling of any kind, nor any logging. It just automates the procedures outlined in the manual with some degrees of freedom. Please be careful when using it. It may kill your kittens and/or burn your house down, but worst of all, it will tend to make you lazy regarding the inner workings of BayPass. The script takes no arguments, but all the variables you should need to edit are presented at the start of the script, coupled with a short description.

Variables

In the beginning of the script there are several line with empty variables. You should fill in the correct values for your case in order to use it. Each option is pretty much self documented with both an explanation of what is expected and an example.