Question: Goseq package in R:getting terms after using getgo
0
gravatar for GabrielMontenegro
3.3 years ago by
United Kingdom
GabrielMontenegro520 wrote:

I have a simple gene vector and trying to get the GO terms using the goseq package from Bioconductor in R.

In this example just one gene:

> unique(d$genes[1])
> [1] "SMARCC1"

> head(stack(getgo(unique(d$genes[1]),'hg19','geneSymbol',fetch.cats=c("GO:BP"))))

      values     ind
1 GO:0006139 SMARCC1
2 GO:0006325 SMARCC1
3 GO:0006333 SMARCC1
4 GO:0006337 SMARCC1
5 GO:0006338 SMARCC1
6 GO:0006351 SMARCC1

Now that I have the GO numbers, is there a way to get the GO terms? That is the exact biological process?

I saw this post which somehow had the GO terms after for each GO value, but I couldn't figure out where he got them.

go bioconductor R • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Benn6.9k • written 3.3 years ago by GabrielMontenegro520
0
gravatar for Parham
3.3 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

I have an annotation file for the organism that I work with that holds GO numbers and their corresponding name. If you have something like that it should be easy to extract terms from that. Otherwise I guess you should look for such an annotation file. Probably it is available on Gene Ontology Consortium.

ADD COMMENTlink written 3.3 years ago by Parham1.4k

I was checking the GO consortium website, but couldn't find a table with that information. Would you mind showing me where I can get this info?

ADD REPLYlink written 3.3 years ago by GabrielMontenegro520
0
gravatar for Benn
3.3 years ago by
Benn6.9k
Netherlands
Benn6.9k wrote:

In the newest version of goseq, you get a table after using the goseq function which conatins the term column. You can use these to match with you head-stack table.

ADD COMMENTlink written 3.3 years ago by Benn6.9k

I just downloaded the latest version, but after running goget I get a list including the genes and the GO terms for every gene. Could you show me the exact function?

ADD REPLYlink written 3.3 years ago by GabrielMontenegro520

I was talking about the goseq function in the package, this is to do the enrichment analysis.

For example:

pwf=nullp(gene.vector,"hg19","geneSymbol")

GO.wall=goseq(pwf,"hg19","geneSymbol",use_genes_without_cat=TRUE)

The object GO.wall is a data frame which contains a column term. You can merge this further in R with your head-stack-getgo object.

ADD REPLYlink written 3.3 years ago by Benn6.9k
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