Search code examples
rbiomart

Get gene location from gene symbol and ID

I want to get gene location of human genome from gene symbol(example: TTN) and gene ID(example: ENSG00000155657). I want to do it using biomaRt package of R. How can I do that?

Solution

  • I'm not entirely sure what you mean by gene location, but I think the following should get you started:

    ensembl <- useMart("ensembl")
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
getBM(attributes=c('chromosome_name', 'start_position', 'end_position', 'strand'),
      filters=c('hgnc_symbol', 'ensembl_gene_id'),
      values=list('TTN', 'ENSG00000155657'),
      mart=ensembl)

    You can input more filters by adding additional vectors (of length two in this example) to the values list.

    You can use the function listAttributes(ensembl) to get a data.frame containing all attributes that you can obtain from biomart.

    As @neilfws has already stated, the biomaRt user guide is the right place to look for more information about biomaRt. I recommend that you ask further questions about Bioconductor R packages like biomaRt on the Bioconductor support forum.