Hi Aditya, you could check the more recent ensembldb EnsDb databases to see if there is something in them you might need/want. I've added protein annotations to them (as provided by Ensembl). They contain the Ensembl protein domains, the AA sequence, all protein domain families (as defined/linked in Ensembl) and the mapping from Ensembl protein IDs to Uniprot (which is unfortunately not always 1:1) - and you get the mapping to the encoding transcripts for free ;)
To play around with it I suggest you get one of the EnsDb databases from AnnotationHub: library(AnnotationHub) query(AnnotationHub(), "EnsDb.Hsapiens") and fetch one of those. Have also a look at the ensembldb vignette(s) for starters. cheers, jo On 09/13/2017 07:02 AM, Aditya Bhagwat wrote: > Hey guys, > > I love the org.Hs.eg.db package (and similar others for other organisms). > > I work a lot with LCMSMS proteomics data, and I have always missed a similar > org.Hs.uniprot.db package, so I am thinking of creating that (and then > sharing it on BioC, to benefit fellow proteomics R users). > > Would you agree that this is of general interest? (Or does this in some form > already exist and have I overlooked it?) > > Thanks for your feedback! > > Cheers, > > Aditya > > > > Disclaimer: This email and its attachments may be confidential and are > intended solely for the use of the individual to whom it is addressed. If you > are not the intended recipient, any reading, printing, storage, disclosure, > copying or any other action taken in respect of this e-mail is prohibited and > may be unlawful. If you are not the intended recipient, please notify the > sender immediately by using the reply function and then permanently delete > what you have received.. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
