ReactomePA:enrichPathway error in universe parameter
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@datafanatic-12212
Last seen 11 months ago

Hi, I'm running the enrichPathway function:

x<-enrichPathway(gene=df$name, organism = "fly", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2, universe, minGSSize = 10, maxGSSize = 500, readable = FALSE)

and I get the error:

universe is not in character and will be ignored...

How is the universe parameter set? My understanding is that I don't have to pass any arguments but it seems that the background genes are not in character format? How is this function accessing the background genes?

enrichPathway ReactomePA • 324 views
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@kevin
Last seen 12 hours ago
Republic of Ireland

Posted on Biostars, too: https://www.biostars.org/p/434669/

[just doing this to connect up and help both communities]

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