Entering edit mode
You can do something like:
library(gage)
data(korg)
head(korg)
korg[grep("cryptococcus", korg[,2], ignore.case=T),]
then you can see 2 strains under species "Cryptococcus neoformans":
cne and cnb.
kg.cne=kegg.gsets(species ="cne"). To generate the gene set:
kegg.cne=kg.cne$kg.sets[kg.cne$sigmet.idx]
length(kegg.cne)
lapply(kegg.cne[1:3], head)
More details, you may read page 6 of the gaege tutorial, for function
documentation do:
?kegg.gsets
HTHs.
--------------------------------------------
On Mon, 6/2/14, Jean.wrote:
Hi Weijun,
Hope you?re doing well.
I?m helping the RNA-Seq analysis for a fungi species,
cryptococcus_neoformans. Do you know if the gene set data
contain this species and how do I find out?
Thanks,
Jean
?
