Goseq package in R:getting terms after using getgo
0
0
Entering edit mode
@javiermendoza-9582
Last seen 8.7 years ago

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][1] which somehow had the GO terms after for each GO value, but I couldn't figure out where he got them.

  [1]: Print to txt file in specific way

R bioconductor gene ontology • 1.6k views
ADD COMMENT

Login before adding your answer.

Traffic: 712 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6