Re: [Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

2015-01-13 Thread Hervé Pagès
Hi, On 01/13/2015 10:22 AM, Marc Carlson wrote: Hi Peter, I would add that you can see a listing all the currently pre-manufactured TxDb packages here: http://www.bioconductor.org/packages/devel/BiocViews.html#___TxDb And for convenience you can also use an OrgansimDb package to connect the c

Re: [Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

2015-01-13 Thread Peter Langfelder
Thanks all! On Tue, Jan 13, 2015 at 10:22 AM, Marc Carlson wrote: > Hi Peter, > > I would add that you can see a listing all the currently pre-manufactured > TxDb packages here: > > http://www.bioconductor.org/packages/devel/BiocViews.html#___TxDb > > And for convenience you can also use an Organ

Re: [Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

2015-01-13 Thread Marc Carlson
Hi Peter, I would add that you can see a listing all the currently pre-manufactured TxDb packages here: http://www.bioconductor.org/packages/devel/BiocViews.html#___TxDb And for convenience you can also use an OrgansimDb package to connect the contents of the TxDb package with the older org

Re: [Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

2015-01-13 Thread James W. MacDonald
Hi Peter, This isn't a devel question. Next time please ask this sort of thing on the support site. As for the message, it seems pretty clear to me. The org.Hs.eg.db package doesn't have the chromosomal location data any more, but the relevant TxDb package does have those data, in a much more use

[Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

2015-01-12 Thread Peter Langfelder
Hi all, can anyone please explain or point me to an explanation of how to replace org.Hs.egCHR and friends that appear to be deprecated in the devel version? The deprecation message isn't very helpful. Thanks! x = org.Hs.egCHR Warning message: In (function () : org.Hs.egCHR is deprecated. Plea