[BioC] Difference between go, with_go and with_go_go

[Marc Carlson]

Hi Konika,

It is not a "BiomaRt solution", but here is one way you can get this 
information by using the org.Hs.eg.db package:

library(org.Hs.eg.db)
get("GO:0003677", org.Hs.egGO2EG)

I am sure you can make biomaRt get you this information too if you 
really want to do it that way.

   Marc



On 12/19/2011 10:48 AM, konika chawla wrote:
> Hi,
> I want to retrieve all human genes annotated with specific go_ids like
> GO:0003677
>
> in the listFilters option I see 3 filters -
> 1) go- it is giving genes even with other go ids not in the query
> 2) with_go  and with_go_go giving error that
>
> Error in getBM(attributes = c("go_id", "name_1006", "entrezgene", "hgnc_symbol",  :
>    biomaRt error:  with_go_go  is a boolean filter and needs a corresponding logical value of TRUE or FALSE to indicate if the query should retrieve all data that fulfill the boolean or alternatively that all data that not fulfill the requirement should be retrieved.
>
>
> Can you tell what is the difference between the three and which is the best option t be used.
> script I used
> tf<-read.table("tf_selection_criteria.csv",sep=",",header=TRUE)
> library(biomaRt)
> mart=useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
> getBM(attributes=c("entrezgene"))
> data<-getBM(attributes=c("go_id","go","name_1006","entrezgene","hgnc_symbol","external_gene_id"),filters="go",values=tf[,2], mart=mart)
>
> Thanks
>
> Konika Chawla
> PhD candidate
> Department of Biology
> NTNU
>
>
>
>
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>
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