[BioC] GAGE RNA-Seq analysis for for a fungi species cryptococcus_neoformans

[Luo Weijun]

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.

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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