Description Usage Arguments Examples
create an topGodata object
1 2 | topGODataNew(selectedSet, backgroundSet, mapping, ontology = "BP",
description = "Simple session", nodeSize = 5)
|
selectedSet |
selectedSet |
backgroundSet |
backgroundSet |
mapping |
mapping |
ontology |
ontology to use |
description |
description |
nodeSize |
nodeSize |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | library(topGOUniProt)
tmp <-uniprotTable2ProteinGOTable(ontology="CC",mapping=getMouseData(PE=1))
head(tmp)
protID <- unique(tmp[,1])
protIDbackground <- unique(tmp[1:200,1])
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1), ontology="BP" )
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1) , ontology="MF")
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1) , ontology="CC")
tmp <- getHumanData(PE=1)
head(tmp)
protIDbackground <- unique(tmp[,"Entry"])
length(protIDbackground)
protID <- protIDbackground[1:100]
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getHumanData(PE=1) , ontology="BP")
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getHumanData(PE=0) , ontology="MF")
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getHumanData(PE=0) , ontology="CC")
summary(res)
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