ReactomePA:enrichPathway error in universe parameter
2
0
Entering edit mode
DataFanatic ▴ 10
@datafanatic-12212
Last seen 3.0 years 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 • 1.3k views
ADD COMMENT
1
Entering edit mode
@kevin
Last seen 1 day ago
Republic of Ireland

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

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

ADD COMMENT
0
Entering edit mode
landenshanie ▴ 40
@landenshanie-23570
Last seen 12 months ago
Australia

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.

ADD COMMENT

Login before adding your answer.

Traffic: 501 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6