Question: Annotation dbi error GO term
0
gravatar for Stane
2.1 years ago by
Stane40
Stane40 wrote:

Hi I am getting this error with the following code, the go key 

AnnotationDbi::select(org.Hs.eg.db, keys='GO:1990281',
                        columns = c("SYMBOL"),
                        keytype = "GOALL")

 

error message : 

None of the keys entered are valid keys for 'GOALL'

my guess is this particular go term only contains proteins and no genes,  the error message seems misleading ?  

 

 

go annotationdbi • 580 views
ADD COMMENTlink modified 2.1 years ago by James W. MacDonald51k • written 2.1 years ago by Stane40
Answer: Annotation dbi error GO term
0
gravatar for James W. MacDonald
2.1 years ago by
United States
James W. MacDonald51k wrote:

As far as I can tell, an efflux pump complex is something that exists in prokaryotes. You are searching the human annotation package for gene symbols based on a GO term that applies to prokaryotes, so by definition that GO term should not be a valid key (e.g., under the hood you are doing an inner join between the Entrez Gene IDs for human to the respective GO terms. Since that GO term doesn't have a corresponding human Entrez Gene ID, the term is invisible to the org.Hs.eg.db package).

But it does exist in the GO.db package:

> select(GO.db, "GO:1990281", "DEFINITION", "GOID")
'select()' returned 1:1 mapping between keys and columns
        GOID
1 GO:1990281
                                                                       DEFINITION
1 A protein complex that is capable of efflux transmembrane transporter activity.
ADD COMMENTlink written 2.1 years ago by James W. MacDonald51k
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