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.calog...@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.calog...@unito.it
>> raffaele.calog...@gmail.com
>> www: http://www.bioinformatica.unito.it
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel@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.calog...@unito.it
raffaele.calog...@gmail.com
www: http://www.bioinformatica.unito.it
[[alternative HTML version deleted]]
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