While we tried as much as possible to reproduce the biomaRt interface, there are some differences between the two packages, and limitations that we won’t be able to overcome.
species / speciesL argumentIn biomaRt, the mart argument was used to specify the
database to connect to, this usually contained some information about
the species of interest. This enabled for example the conversion of gene
symbols to Ensembl gene IDs (since multiple species can have the same
gene symbol). In remart, the mart argument is no longer
required, and the species of interest is specified via the new
species argument in getBM() and
speciesL argument in getLDS().
version argumentIn biomaRt, the Ensembl version to query could be specified with the
version argument (or directly in the host
argument) in useEnsembl(). In remart, the
version argument is now available in all functions that
query Ensembl, and it is used to specify the Ensembl release to query.
If not specified, the latest release will be used.