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Old 11-27-2013, 06:41 AM   #6
bigmw
Senior Member
 
Location: US

Join Date: Aug 2013
Posts: 123
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The code I give you has been tested across multiple platforms. Below is what I got on my computers. No sure what happened on your side.
You seem to have many odd problems with your computer based on your previous questions/notes. I would suggest you either find another computer or clean up your system (if you can) and resintall the updated R/Bioconductor, gage, pathview and other package from scratch. This will make your work much easier.

> kg.ame=kegg.gsets("ame")
> lapply(kg.ame, head, 3)
$kg.sets
$kg.sets$`ame00010 Glycolysis / Gluconeogenesis`
[1] "408559" "408654" "409624" "409773" "410122" "411140" "411188" "411576" "411897" "412362" "412522" "412843" "413924"
[14] "550687" "550785" "551005" "551039" "551103" "551154" "551631" "552007" "552086" "552678" "552736" "724724" "725455"
[27] "726117" "726225" "727153" "727456"

$kg.sets$`ame00020 Citrate cycle (TCA cycle)`


$sigmet.idx
[1] 76 82 83

$sig.idx
[1] 76 82 83

$met.idx
[1] 1 2 3

$dise.idx
integer(0)
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