Hi Raffaele,
This problem should be resolved in devel at this time. Please update to
the latest version of AnnotationDbi (1.27.14) and try again.
Marc
On 09/23/2014 02:36 PM, calogero UNITO wrote:
affaeleaffaeleHi 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
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