Specify Ensembl Plant version

[timedreamer]

Hello,
Really great package. It's now part of my working flow for all analysis. I'm working with plants, so I use Ensembl Plant a lot. One thing I'm curious is: is there any way to specify the release version of Ensembl Plant?

Similar with Ensembl, Ensembl Plant also updates regularly. I want to keep my result replicable, in case they update their database. For example, in the newest Release 40, the Setaria italica genome was updated. It seems they do have several archived sites, like Release 35 and Release 37.

An example of my code to retrieve gene description is below. It would be awesome if the version info could be implemented (maybe it's already done?)

biomart(genes = gene_list),
       mart = "plants_mart",
       dataset = "zmays_eg_gene",
       attributes = c("description",
                      "external_gene_name", "external_gene_source"),
       filters = "ensembl_gene_id")

Thank you!!

Best,
Ji

[HajkD]

Hi Ji,

I am very happy that biomartr is useful for your research and thank you very much for
making such a great suggestion.

I will gladly implement a new argument release in the biomart() function (as well as in all get*()) functions to make it even easier to reproducibly retrieve data from different releases.

I will keep you posted here and will write you as soon as I have the new functionality embedded in the new biomartr version.

Many many thanks for your great feedback! I truly appreciate it :)

Cheer,s
Hajk

[timedreamer]

Hi Hajk,
Just wonder whether there is any updates on the ensembl version functionality?

Best,
Ji

[Roleren]

See discussion:

#45

So @HajkD , will the new PR, solve this issue too ?

[HajkD]

Yes absolutely! Thanks to your pr this is now resolved. @timedreamer please let us know if it works for you?

[HajkD]

I assume this has been solved.