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://stat.ethz.ch/mailman/listinfo/bioc-devel
