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Question: BiomaRt returns 0 obs
0
gravatar for edelman
3 months ago by
edelman0
edelman0 wrote:

I have been running some code in R to make a data frame with my ENST IDs and corresponding gene symbols. I have used the following code before but I have been unable to generate this table recently. The problem is that getBM returns 0 observations. Any help would be appreciated. Perhaps known issues with getBM? 

 

mart<- useDataset("hsapiens_gene_ensembl", useMart('ensembl'))

genes<-Data1$Name


G_list<-getBM(filters
  = "ensembl_gene_id", attributes = c("ensembl_gene_id",
  "external_gene_name", "description"), values = genes, mart = mart)

My code, which does not produce any errors, runs and returns an empty object 0 observations with 2 columns. Genes is a list of ENST IDs. 

 

Thanks,

Bill 

ADD COMMENTlink modified 3 months ago by James W. MacDonald48k • written 3 months ago by edelman0

I'm using R version "Feather Spray" v. 3.5.1. Also doesn't work on previous major release. 

ADD REPLYlink modified 3 months ago • written 3 months ago by edelman0
2
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald48k wrote:

You will have to show some reproducible code that shows the problem.

> library(biomaRt)
> library(org.Hs.eg.db)

> ensids <- head(keys(org.Hs.eg.db, "ENSEMBL"))
> ensids
[1] "ENSG00000121410" "ENSG00000175899" "ENSG00000256069" "ENSG00000171428"
[5] "ENSG00000156006" "ENSG00000196136"
> mart <- useMart("ensembl","hsapiens_gene_ensembl")
> getBM(c("ensembl_gene_id","external_gene_name","hgnc_symbol","description"), "ensembl_gene_id", ensids, mart)
  ensembl_gene_id external_gene_name hgnc_symbol
1 ENSG00000121410               A1BG        A1BG
2 ENSG00000156006               NAT2        NAT2
3 ENSG00000171428               NAT1        NAT1
4 ENSG00000175899                A2M         A2M
5 ENSG00000196136           SERPINA3    SERPINA3
6 ENSG00000256069              A2MP1       A2MP1
                                                         description
1             alpha-1-B glycoprotein [Source:HGNC Symbol;Acc:HGNC:5]
2           N-acetyltransferase 2 [Source:HGNC Symbol;Acc:HGNC:7646]
3           N-acetyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:7645]
4              alpha-2-macroglobulin [Source:HGNC Symbol;Acc:HGNC:7]
5          serpin family A member 3 [Source:HGNC Symbol;Acc:HGNC:16]
6 alpha-2-macroglobulin pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:8]

You do state that the genes object is a list of ENST IDs. If I were to infer that by ENST ID you mean Ensembl transcript IDs, then you need to use ensembl_transcript_id rather than ensembl_gene_id.

ADD COMMENTlink written 3 months ago by James W. MacDonald48k
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