annotation - biomaRt - Error in UseMethod

Question

[ferreira.cristina]

Hi,

I try run the getBM from biomaRt but a error was returned.

ensembl=useMart("ENSEMBL_MART_ENSEMBL")

ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

 list <- c("DUOX2", "DIRAS3")

x <- getBM(attributes = c("ensembl_gene_id","external_gene_name", "gene_biotype", 
                             "description", "chromosome_name","start_position","end_position",
                             "transcript_gencode_basic"),
              filters ='external_gene_name', values=list,mart = ensembl)

Error in UseMethod("filter_") : 
  método não aplicável para 'filter_' aplicado a um objeto de classe "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"

[Hamid Ghaedi]

Your code seems Ok to me and using that I got the intended result. Mybe you need to update some of your package installation (see this post )or detach all package except biomaRt, and do analysis.

[Kevin Blighe]

I have not had any problem here:

  ensembl_gene_id external_gene_name   gene_biotype
1 ENSG00000162595             DIRAS3 protein_coding
2 ENSG00000140279              DUOX2 protein_coding
3 ENSG00000140279              DUOX2 protein_coding
                                              description chromosome_name
1 DIRAS family GTPase 3 [Source:HGNC Symbol;Acc:HGNC:687]               1
2      dual oxidase 2 [Source:HGNC Symbol;Acc:HGNC:13273]              15
3      dual oxidase 2 [Source:HGNC Symbol;Acc:HGNC:13273]              15
  start_position end_position transcript_gencode_basic
1       68045886     68051631            GENCODE basic
2       45092650     45114172            GENCODE basic
3       45092650     45114172

I am using R 4.0.3 and biomaRt v2.45.9

[soniabedi.07]

I am facing similar error. Could you get a solution for above?

[Kevin Blighe]

Please show the exact code that you're running, the error(s) produced, and also the output of sessionInfo(). Thank you.