There were 18 genes missing, due to a filtering step that went awry.
> select(org.Hs.eg.db, z, "SYMBOL")
'select()' returned 1:1 mapping between keys and columns
ENTREZID SYMBOL
1 1665 DHX15
2 6819 SULT1C2
3 8449 DHX16
4 27233 SULT1C4
5 80273 GRPEL1
6 134266 GRPEL2
7 195814 SDR16C5
8 729059 TEX46
9 100506895 LUARIS
10 110121294 LOC110121294
11 110121295 LOC110121295
12 110121296 LOC110121296
13 114827811 LOC114827811
14 114827812 LOC114827812
15 114827813 LOC114827813
16 114827814 LOC114827814
17 114827815 LOC114827815
18 114827816 LOC114827816
> sessionInfo()
R Under development (unstable) (2024-03-12 r86109)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /home/ubuntu/downloads/R-devel/lib/libRblas.so
LAPACK: /home/ubuntu/downloads/R-devel/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] org.Hs.eg.db_3.19.1 AnnotationDbi_1.65.2 IRanges_2.37.1
[4] S4Vectors_0.41.5 Biobase_2.63.0 BiocGenerics_0.49.1
These new packages are still on the builder, and have to be transferred over to
the download repository, which I imagine will happen sometime next week.
Best,
Jim
From: Anatoly Sorokin <lpto...@gmail.com>
Sent: Thursday, April 18, 2024 11:01 PM
To: James W. MacDonald <jmac...@uw.edu>
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene
Great! Thank you! On Fri, Apr 19, 2024 at 2: 29 AM James W. MacDonald <jmacdon@
uw. edu> wrote: There was an error in the scripts used to generate the organism
packages that excluded (among other genes) GRPEL1. We have rectified the error
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Great!
Thank you!
On Fri, Apr 19, 2024 at 2:29 AM James W. MacDonald
<jmac...@uw.edu<mailto:jmac...@uw.edu>> wrote:
There was an error in the scripts used to generate the organism packages that
excluded (among other genes) GRPEL1. We have rectified the error and are
re-running. The updated packages should be available early next week.
-----Original Message-----
From: Bioc-devel
<bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> On
Behalf Of James W. MacDonald
Sent: Thursday, April 18, 2024 9:30 AM
To: Anatoly Sorokin <lpto...@gmail.com<mailto:lpto...@gmail.com>>;
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene
It is the wrong place to send the request. This listserv is for package
developers. If you want support please use
support.bioconductor.org<https://urldefense.com/v3/__http:/support.bioconductor.org__;!!K-Hz7m0Vt54!mJ3Pa4pX6JJKDHxEwVlqoHpn2SjbdVeSm1duor0h0YuSpIVdzercsgEfkXrkQHSZYc8xFsB3FC-Jqg$>.
-----Original Message-----
From: Bioc-devel
<bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> On
Behalf Of Anatoly Sorokin
Sent: Thursday, April 18, 2024 12:40 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene
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Hi,
sorry if this is the wrong list to send this request, but the landing page of
the org.Hs.eg.db package contains no reference for the bug report.
The most recent version of the org.Hs.eg.db package (3.19.7) misses the GRPEL1
gene
(https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/gene/80273__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnmYBzl1CQ$<https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/gene/80273__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnmYBzl1CQ$>
). It could not be found either by SYMBOL, or by ENTREZID:
> orgDB = org.Hs.eg.db
> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'ENTREZID'. Please use the keys
method to see a listing of valid arguments.
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'SYMBOL'. Please use the keys
method to see a listing of valid arguments.
however, in the previous version of the package (3.18.0), it could be found by
both keys:
> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
'select()' returned 1:1 mapping between keys and columns
ENTREZID SYMBOL GENENAME
1 80273 GRPEL1 GrpE like 1, mitochondrial
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
'select()' returned 1:1 mapping between keys and columns
SYMBOL GENENAME ENTREZID
1 GRPEL1 GrpE like 1, mitochondrial 80273
That omission caused an error in our BioNAR package. As this is the only
missing gene in the network for the time being I've fixed this manually in the
vignette, but I'd like to understand is it a real mistake or am I using the
package in the wrong way?
Cheers,
Anatoly
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