[Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

[Anatoly Sorokin]

Great!
Thank you!

On Fri, Apr 19, 2024 at 2:29 AM James W. MacDonald <jmacdon using 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-bounces using r-project.org> On Behalf Of James W.
> MacDonald
> Sent: Thursday, April 18, 2024 9:30 AM
> To: Anatoly Sorokin <lptolik using gmail.com>; bioc-devel using 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.
>
> -----Original Message-----
> From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Anatoly
> Sorokin
> Sent: Thursday, April 18, 2024 12:40 AM
> To: bioc-devel using 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$
> ). 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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