topGO allGenes argument

Question

[Ric]

Hi, In this paper they used the following to determine differential expression

> tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5))
> topTags(tr)
Coefficient:  -1*Leaves.2 1*Leaves.3
          logFC unshrunk.logFC logCPM  PValue     FDR
sp0090975   2.6            2.6    2.8 5.7e-14 2.7e-09
sp0037632  -3.0           -3.0    3.4 1.7e-13 2.7e-09
sp0074153  -3.9           -3.9    3.8 1.8e-13 2.7e-09
sp0008306   3.2            3.2    2.9 1.8e-13 2.7e-09
sp0073530  -4.5           -4.5    3.4 2.3e-12 2.3e-08
sp0025713  -3.9           -3.9    4.4 2.6e-12 2.3e-08
sp0037721   7.8            8.0    2.4 2.7e-12 2.3e-08
sp0083660   2.0            2.0    4.4 3.2e-12 2.3e-08
sp0052245  -2.9           -2.9    4.9 3.9e-12 2.6e-08
sp0071520  -3.3           -3.3    2.7 5.8e-12 3.4e-08

How is it possible to get the gene names (1st column) out of tr and give them as argument to topGO's allGenes?

myGOdata <- new("topGOdata", description="My project", ontology="BP", allGenes=geneList,  annot = annFUN.gene2GO, gene2GO = geneID2GO)

Thank you in advance.

Answer 1

[e.rempel]

Hi

you could use:

rownames(topTags(tr)@.Data[[1]])

[Ric]

It turns out that allGenes should be a R vector which contains the

• gene names and
• p-value

How to convert tr (1st and 5th column) to an vector?

[Kevin Blighe]

geneList <- tr$PValue

names(geneList) <- tr[,1]

...or names(geneList) <- rownames(tr) if the gene IDs are rownames of tr.