Hi Leonard, Hi Herve,
I followed your conversation, since I have noticed the same problem. Thanks,
Herve, for the explanation of the recent changes on hg19.
The GRCh37.P13 report states in its last line:
MT assembled-molecule MT Mitochondrion J01415.2=
Hi Leonard,
On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
Dear Bioc team,
I'm following up on this recent GitHub issue
Glad to help!
On Thu, Aug 13, 2020 at 5:51 PM Margolin, Gennady (NIH/NICHD) [C] <
gennady.margo...@nih.gov> wrote:
> Hi Jim,
>
>
>
> Hi Jim,
>
>
>
> Awesome, that makes sense now. I was wondering whether org.Dr.eg.db has
> only functional annotation, which I thought it was as it did not refer to
Hi Jim,
Hi Jim,
Awesome, that makes sense now. I was wondering whether org.Dr.eg.db has only
functional annotation, which I thought it was as it did not refer to a specific
genome, unlike TxDb packages, but then I found what I said in my previous
emails.
Thank you very much,
Gennady
From:
Hi Gennady,
That information should probably be cleaned up, and the BiMaps that point
to the location data removed. While the OrgDbs do contain position
information, it's been deprecated, which you would find if you tried to
query using select():
> select(org.Dr.eg.db, "30037", "CHR")
'select()'
Hi Vincent,
Thank you for responding.
Here is from the R documentation help page from this package (I have version
3.10.0 (I doubt anything changed with the latest one, which is 3.11.4)):
-
org.Dr.egCHRLOC {org.Dr.eg.db}
Entrez Gene IDs to
This should probably be posed to the support site. What version of the
package are you using? Where
are you seeing coordinates? I would expect those to be obtained from the
TxDb package, or perhaps
from AnnotationHub.
> columns(org.Dr.eg.db)
[1] "ACCNUM" "ALIAS""ENSEMBL"
Hello,
I have a short question – how do I figure the genome version for org.Dr.eg.db
package? I couldn’t see it in the DESCRIPTION and also it’s not in
org.Dr.eg_dbInfo() output. It would be nice to know if this is danRer11/GRCz11
or some other assembly, as there are coordinates present in the
