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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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pathfindR using proteomics data #148

Closed lyons89 closed 1 year ago

lyons89 commented 1 year ago

Hello Ege,

I'm a fan of pathfindR and use it all the time for my proteomics pathway analysis needs. I had a quick question about the enrichment analysis that pathfindR performs. Based on my limited experience it looks like you use ORA for the pathway analysis step. I was wondering since in proteomics we never identify all the proteins in a sample if the background should be changed to only include proteins that were identified in the analysis. I don't know if you have any experience with proteomics pathway enrichment but I'd like to hear your opinion on it.

Best, Scott

egeulgen commented 1 year ago

Hello Scott,

By default, the background for ORA is the set of all proteins in the PIN. So my suggestion would be to use a subset of the PIN to only contain proteins identified in your analysis (hence using a custom PIN, you can read more about that in the vignettes).

Hope this helps, Best, -E

ozanozisik commented 1 year ago

Hello, Currently changing the PIN is the only way to change the background genes in pathfindR however it is not a good way as the interactions are there (as a priori information) even if you do not measure. We will add an argument soon to change the background gene set in ORA. Thank you for highlighting this. Best, Ozan

Apirog9 commented 10 months ago

Is this currently possible to define a background?