Is there a function pagoo_2_roary ?

[diaspj]

Hello to the pagoo team,

First, my congratulations on the great work made on the development of pagoo R library.

The main question I want to put in this forum is in the following:

1. Is there a easy and quick way of converting the pagoo pangenome object into the gene_presence_absence_csv output file and other important output files generated by roary?

2. If not, are there plans to make available?

3. If there are no plans to make it available, is it possible for the pagoo team to leave some quick indications on how to construct the gene_presence_absence_csv and other important roary output files in an easy and quick way from the pagoo pangenome R6 class object, PgR6MS.

I don't have much knowledge on the internal way how roary generates these output files and which ones are important to allow being used as input by other downstream softwares.

The reasoning for being useful the generation of this gene_presence_absence_csv file is in case pagoo does not make available a certain function that might be useful in the analysis of the Pangenome of a given bacterial species but other post-processing software do, the pagoo users might have an easy access to these functions.