problem with extracting special gene sets from kegg gene sets for gage

[wmseq]

Hi bigmw,
With your help, I have downloaded the whole pathway gene sets for honey bees from Kegg successfully. However, when I tried to extract the signaling/metabolic pathway using the command given by you, it seems that something was wrong with the command, because I just got a file of 78 bytes.

This is the command I used:
kegg.gs=kg.ame$kg.sets[kg.ame$sigmet.idx]

How can I check if kegg.gs is right?


Thanks a lot!!

Richard

[bigmw]

I assume you’ve done the following:
library(gage)
kg.ame=kegg.gsets("ame")

then do:
lapply(kg.ame, head, 3)
lapply(kg.ame, length)

And post the output here.