[BioC] How to create a GO2gene object for topGO?

[michael watson (IAH-C)]

This code might work.

In this example, my data is in a data.frame, called array2go.

The column "Accn" contains the identifier for spots on the array
The column "GO_ID" contains the GO identifier.
The column "Category" contains the GO category.

geneNames is all Accns on the array
sigGenes is the significant set

mf <- array2go[array2go$Category=="Function",]
mygene2GO <- sapply(unique(as.vector(mf$Accn)), 
                    function(x)
as.character(unique(mf$GO_ID[mf$Accn==x])))
geneNames <- unique(array2go$Accn)
sigGenes # this comes from somewhere!

geneList <- factor(as.integer(geneNames %in% sigGenes))
names(geneList) <- geneNames

GOdata <- new("topGOdata",              
              ontology="MF",             
              allGenes=geneList,        
              annot=annFUN.gene2GO,    
              gene2GO=mygene2GO)      

test.stat <- new("classicCount",             
                 testStatistic=GOFisherTest, 
                 name="Fisher Test")         
                 
resultFis <- getSigGroups(GOdata, test.stat) 

res <- GenTable(GOdata, classic=resultFis, topNodes=288)
res[1:10,]

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Quin Wills
Sent: 23 October 2008 23:18
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] How to create a GO2gene object for topGO?

Hello all

I have some significant Illumina v1 gene expression probes (and their 
probe 'universe') I want to  run GO enrichment analysis on.

I assume that:
(i)  I need illumnaHumanv1.db for the GO2PROBE mappings
(ii) I need to to create a GO2gene object for input into topGO as:
new("topGOdata", ontology="BP", allGenes=my.probe.list, 
annot=annFUN.GO2genes, GO2gene=my.GO2gene)

I'm just not joining the mental dots dots between (i) and (ii). Or am I 
completely missing the point? Any quick/simple guidance to get from my 
probes to a topGOdata object would be very, very welcome - thanks!

Quin **

* *

* *

*Quin Wills*
*DPhil candidate*

* *

*Department of Statistics*

*University** of Oxford***

*1 South Parks Road*
*Oxford***

*OX1 3TG
United Kingdom*

 

*01865 285 394*


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