Great! Thank you! On Fri, Apr 19, 2024 at 2:29 AM James W. MacDonald <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> On Behalf Of James W. > MacDonald > Sent: Thursday, April 18, 2024 9:30 AM > To: Anatoly Sorokin <lpto...@gmail.com>; 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. > > -----Original Message----- > From: Bioc-devel <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 > Subject: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene > > !-------------------------------------------------------------------| > This Message Is From an Untrusted Sender > You have not previously corresponded with this sender. > See https://itconnect.uw.edu/email-tags for additional > information. Please contact the UW-IT Service Center, > h...@uw.edu 206.221.5000, for assistance. > |-------------------------------------------------------------------! > > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnkLvQOPWA$ > > _______________________________________________ > Bioc-devel@r-project.org mailing list > > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!gVVVvLvwzIeBrPusP589IFjHSBtLnX6o2IYh-GkVcdCXwhp_bDFM8274jULdJPvUWEfh_31If7xjrYI$ > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
