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Hey Pedro,
I've been away for a while with the package maintenance, but I've fixed some things again this week. I'm so sorry for taking a long time to answer you.
Thank you very much for your interest in the package!
About your question, I assume that the user will use the PCIT and RIF functions independently to be able to manipulate the input for the following steps, such as running the PCIT first and then running the RIF.
In the main function of the package (runAnalysis), I do a differential expression between the two conditions to filter out only the most significant genes. From these genes, I calculate the RIF and then the PCIT.
I hope I have answered your question!
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