[Bioc-devel] deprecated org.Hs.egCHRLOC UPDATE: the as.list() behaves differently in stable and devel configuration

[calogero UNITO]

Hi Vincent,
I have further investigated the error I have in the vignette of chimera 
devel package .
It is related to the libraries used to access to org.Hs.eg.db in the 
devel branch.

In the presence of the following libraries (stable branch):
[1] org.Hs.eg.db_2.14.0  RSQLite_0.11.4       DBI_0.3.0
[4] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2   Biobase_2.24.0
[7] BiocGenerics_0.10.0  BiocInstaller_1.14.2

If I extract start and end position for the chromosome location from 
org.Hs.eg:
 >chr.tmps <- as.list(org.Hs.egCHRLOC)
 >chr.tmpe <- as.list(org.Hs.egCHRLOCEND)

 >  as.numeric(chr.tmps[1:3])
[1] -58858172  18248755 -43248163
 >  as.numeric(chr.tmpe[1:3])
[1] -58864865  18258723 -43280376

I get different numbers for star and end of a gene.

In case I used the libraries derived from devel branch
[1] org.Hs.eg.db_2.14.0   RSQLite_0.11.4 DBI_0.3.0
[4] AnnotationDbi_1.27.13 GenomeInfoDb_1.1.19 IRanges_1.99.28
[7] S4Vectors_0.2.4       Biobase_2.25.0 BiocGenerics_0.11.5

 > chr.tmps <- as.list(org.Hs.egCHRLOC)
org.Hs.egCHRLOC is deprecated as the data is better accessed from
   another location. Please use an appropriate TxDb object or package for
   this kind of data.
 > chr.tmpe <- as.list(org.Hs.egCHRLOCEND)
org.Hs.egCHRLOC is deprecated as the data is better accessed from
   another location. Please use an appropriate TxDb object or package for
   this kind of data.

 >  as.numeric(chr.tmps[1:3])
[1] -58858172  18248755 -43248163
 > as.numeric(chr.tmpe[1:3])
[1] -58858172  18248755 -43248163

The values associated to start and end of the gene are the same.
This is actually the reason why I get errors in the vignette of chimera 
package.





R 3.1.1:
sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

Then I installed the basic configuration needed to use org.Hs.eg.db in 
the actual stable release:

source("http://bioconductor.org/biocLite.R")
biocLite("org.Hs.eg.db")
library("org.Hs.eg.db")

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base

other attached packages:
[1] org.Hs.eg.db_2.14.0  RSQLite_0.11.4       DBI_0.3.0
[4] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2   Biobase_2.24.0
[7] BiocGenerics_0.10.0  BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] IRanges_1.22.10 stats4_3.1.1    tools_3.1.1



Then I used  the devel release packages:

|library(BiocInstaller)
useDevel()|
library("org.Hs.eg.db")
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] org.Hs.eg.db_2.14.0   RSQLite_0.11.4        DBI_0.3.0
[4] AnnotationDbi_1.27.13 GenomeInfoDb_1.1.19   IRanges_1.99.28
[7] S4Vectors_0.2.4       Biobase_2.25.0        BiocGenerics_0.11.5



On 23/09/14 12:41, Vincent Carey wrote:
> Of note, this is not an error and seems at this time not even to be a
> warning.
> A message is emitted indicating the deprecation, so we have a release to
> figure out how to deal with the fact that the *CHR/*CHRLOC entities will go
> away
> in the next release.
>
> There are various possible workarounds.  Some more commentary will be
> forthcoming.
>
>
> On Tue, Sep 23, 2014 at 3:52 AM, calogero UNITO <raffaele.calogero at unito.it>
> wrote:
>
>> Hi,
>> I am the maintainer of chimera package and I am getting the following
>> error in the develop version:
>>
>> org.Hs.egCHRLOC is deprecated as the data is better accessed from
>>     another location. Please use an appropriate TxDb object or package for
>>     this kind of data.
>>
>> Could please indicate me which package I should used instead of
>> org.Hs.eg.db ?
>>
>> Cheers
>> Raf
>>
>> --
>> ----------------------------------------
>> Prof. Raffaele A. Calogero
>> Bioinformatics and Genomics Unit
>> MBC Centro di Biotecnologie Molecolari
>> Via Nizza 52, Torino 10126
>> Tel.   ++39 0116706457
>> Fax    ++39 0112366457
>> Mobile ++39 3333827080
>> email: raffaele.calogero at unito.it
>>          raffaele.calogero at gmail.com
>> www:   http://www.bioinformatica.unito.it
>>
>>
>>          [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>


-- 
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
Tel.   ++39 0116706457
Fax    ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
        raffaele.calogero at gmail.com
www:   http://www.bioinformatica.unito.it


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