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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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p-adjusted in the output of pathfindR #66

Closed ManarRashad closed 3 years ago

ManarRashad commented 3 years ago

After getting the output of pathfindR, I found lowest p value and highest p value but not find p adjusted

I hope this to be added on the output. till this moment, what should I do to get the p adjusted for each pathway? What I thought to use the p.adjust function in R p.adjust(pvalue,method = "fdr")

Is this right or not? and if not what should I do?

ozanozisik commented 3 years ago

Dear Manar Rashad, Those p-values are already adjusted. The reason of lowest and highest p-value columns is, same term can be enriched in different iterations in different active subnetworks giving different p-values. I personally use the lowest p-values obtained for the terms. Regards, Ozan