ReactomePA enrichPathway function

Question

[ATCG]

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?

Answer 1

[Kevin Blighe]

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/

[ATCG]

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!

[Kevin Blighe]

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.

[Kevin Blighe]

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

• https://github.com/YuLab-SMU/DOSE/blob/master/R/enricher_internal.R#L56-L65

The related GitHub issue:

• https://github.com/YuLab-SMU/clusterProfiler/issues/217

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

[ATCG]

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

Answer 2

[landenshanie]

Check that the universe you input are characters and not numerics. The entrez ID are numbers so R recognizes them as numerics, but this function needs them to be characters.