[Bioc-devel] Use of EnsDb in the AnnotationDbi framework

Morgan, Martin Martin.Morgan at roswellpark.org
Sun Jan 10 18:28:34 CET 2016

Thanks Johannes, this is a valuable contribution and I've added it to the 'official' vignette.

From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Rainer Johannes [Johannes.Rainer at eurac.edu]
Sent: Thursday, January 07, 2016 9:10 AM
To: Bioc-devel
Subject: [Bioc-devel] Use of EnsDb in the AnnotationDbi framework

Dear all,

thanks to Vince’s suggestion I have now implemented the central AnnotationDbi methods “columns”, “keys”, “keytypes” and “select” for EnsDb objects in my ensembldb package version 1.3.11 (EnsDb are TxDb like annotation packages/objects tailored to Ensembl based annotations). Thus, EnsDb based annotation packages can now be used in the AnnotationDbi framework. The methods support in addition also the filter framework of the ensembldb package to provide some more fine grained querying and data retrieval.
I have forked the AnnotationDbi package and added a section to its “IntroToAnnotationPackages.Rnw” vignette describing how to use EnsDb objects along with the above mentioned methods (https://github.com/jotsetung/AnnotationDbi). Eventually this could also be inserted to the “official” AnnotationDbi package.

best, jo
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