How to get cisBP_mouse_pfms_2021.rds in runFigRGRN function?

[Rivers-Lee]

Hello,

Thank you to build this amazing tool, I already build Fruit fly's TSS file & BSgenome to run the runGenePeakcorr function, but to the runFigRGRN, I don't quite sure how to get the cioBP_pfm.rds about the fly.

Could you please tell me how you downloaded and constructed these two pfm matrices from the cisBP database and stored them as rds of this data structure?

[vkartha]

Hey @Rivers-Lee ! So sorry for the delayed reply, I unfortunately am only able to check this from time to time. The mouse and human motif PFMs were originally from cisBP (http://cisbp.ccbr.utoronto.ca/bulk.php), curated by us over the past couple of years (filtered for high quality sequence motifs, collapsed into groups etc.). You should be able to grab the Fly PWM's from Jaspar's database (see as an example https://greenleaflab.github.io/chromVAR/reference/getJasparMotifs.html), if you want to use a custom motif db for fly that's not from Jaspar, it will need parsing to match the format used / expected by chromVAR (PFMatrixList / PWMatrixList object supported via TFBSTools). Hope this helps