topGODataNew: create an topGodata object

Description Usage Arguments Examples

Description

create an topGodata object

Usage

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topGODataNew(selectedSet, backgroundSet, mapping, ontology = "BP",
  description = "Simple session", nodeSize = 5)

Arguments

selectedSet

selectedSet

backgroundSet

backgroundSet

mapping

mapping

ontology

ontology to use

description

description

nodeSize

nodeSize

Examples

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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)

wolski/topGOUniProt documentation built on May 4, 2019, 9:47 a.m.