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rncbibiomart

How to use NCBI gene database in biomaRt R package

I'm not very expert with R but I'm trying to learn ho to use the biomaRt package to find genes located in my regions of interest.

I've managed to produce a valid output using the ensembl dataset with the following code:

> mart= useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
> results <- getBM(attributes =c("chromosome_name","start_position","end_position",
"band","hgnc_symbol","entrezgene"), filters = c("chromosome_name","start","end"),
values = list(1,226767027,227317593), mart=mart)

I know that the "entrezgene" corresponds to the NCBI gene ID, but I would like to have the GENE NAME from NCBI.

Is there a way to use biomaRt connected to NCBI database and retrieve that informartion?

Thank you in advanced.

Solution

  • Type listAttributes(mart) to see the list of attributes you can select

    Regarding gene name, I think you might want external_gene_id but there are other gene name options as well.