ReactomePA enrichPathway function
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2.4 years ago
ATCG ▴ 370

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 errro:

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?

ReactomePA enrichPathway • 2.0k views
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2.4 years ago

Hey DataFanatic. Good to see you here. Does the function not run if you just leave universe out? From what I understand, it is a background list of genes pulled in automatically from an online database, and that it is [presumably] used for the derivation of test statistics. The documentation and examples / vignettes for that package do not reveal too much information.

Just linking up to the post on Bioconductor, too: https://support.bioconductor.org/p/130489/

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Hi Kevin, Thanks for your answer. It works without the universe parameter but I was not sure if leaving it out would automatically pull the background genes in the online database. I have completed these analyses thinking that yes, the background is automatically pulled but I'm not sure that this is the case and my results are too good to be true :) so I need to make sure. Thanks!

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Oh great, yes, I think that it's okay to leave it out. For 99.999% of analyses, the user does not have to worry about this parameter, I think. I checked the function code trail (yesterday) and could see that it does indeed automatically pull the background data in behind the scenes.

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Actually, it is somewhat cryptic. The error is thrown here:

The related GitHub issue:

Irrespective, I am not sure that you need to worry about using this parameter.

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I see. Thanks for checking, its good to know that the background is pulled automatically.