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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Directionality of Fold_Enrichment value #79

Closed amanda-hi closed 3 years ago

amanda-hi commented 3 years ago

When using run_pathfindR, is it possible to identify whether the gene set/pathway term is globally up or down regulated, i.e activated or repressed in the group of interest? I've performed pathway analysis using other tools (ex. the gage Bioconductor package), and they have provided mean change scores or a similar score denoting directionality (+/-) of the enrichment. I know that the agglomerated z-score for each sample & each term can be calculated using the score_terms function, but this is performed per sample, rather than per group (as in case vs. control). Is this mentioned in the docs somewhere, or is this something that pathfindR doesn't do? Or are all enriched terms identified by pathfindR upregulated/activated? Thank you!

egeulgen commented 3 years ago

Hey @aleonti, Unfortunately, this is isn't something that pathfindR does. One can only say that the enriched terms identified by pathfindR are dysregulated. Since this (indicating directionality of the dyregulation) is related to different methodology, we cannot implement this within pathfindR soon but I have noted this as a future enhancement.

In the meanwhile, as you suggest, you may use score_terms() + plot_scores() to have an idea on the up-/down- regulation status of the enriched pathways.

Thank you, -E

amanda-hi commented 3 years ago

The quick reply is much appreciated, thanks so much! pathfindR is a great package!