Parameters query additions

[BaylorSci]

I have checked the document and can't find a way to include addFeatures=True to the R interface of MSGFplus to allow files to be post processed with Percolator. Is this something that can be included?
In that line, would it also be possible to allow the decoy abbreviation to be included/changed in this environment?

[lgatto]

It might not be available, and it's very unlikely that new features will be added. One suggestion would be to construct the commands in R and the run them using the system() function.