[Bioc-devel] Question about org.Dr.eg.db package
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)):
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org.Dr.egCHRLOC {org.Dr.eg.db}
Entrez Gene IDs to Chromosomal Location
Description
org.Dr.egCHRLOC is an R object that maps entrez gene identifiers to the starting position of the gene. The position of a gene is measured as the number of base pairs.
The CHRLOCEND mapping is the same as the CHRLOC mapping except that it specifies the ending base of a gene instead of the start.
??
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This output also does not show any genome version:
org.Dr.eg_dbInfo()
name value 1 DBSCHEMAVERSION 2.1 2 Db type OrgDb 3 Supporting package AnnotationDbi 4 DBSCHEMA ZEBRAFISH_DB 5 ORGANISM Danio rerio 6 SPECIES Zebrafish 7 EGSOURCEDATE 2019-Jul10 8 EGSOURCENAME Entrez Gene 9 EGSOURCEURL ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 10 CENTRALID EG 11 TAXID 7955 12 GOSOURCENAME Gene Ontology 13 GOSOURCEURL ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ 14 GOSOURCEDATE 2019-Jul10 15 GOEGSOURCEDATE 2019-Jul10 16 GOEGSOURCENAME Entrez Gene 17 GOEGSOURCEURL ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 18 KEGGSOURCENAME KEGG GENOME 19 KEGGSOURCEURL ftp://ftp.genome.jp/pub/kegg/genomes 20 KEGGSOURCEDATE 2011-Mar15 21 GPSOURCENAME UCSC Genome Bioinformatics (Danio rerio) 22 GPSOURCEURL 23 GPSOURCEDATE 2017-Nov1 24 ENSOURCEDATE 2019-Jun24 25 ENSOURCENAME Ensembl 26 ENSOURCEURL ftp://ftp.ensembl.org/pub/current_fasta 27 UPSOURCENAME Uniprot 28 UPSOURCEURL http://www.UniProt.org/ 29 UPSOURCEDATE Mon Oct 21 14:32:30 2019 From: Vincent Carey <stvjc at channing.harvard.edu> Date: Thursday, August 13, 2020 at 2:46 PM To: "Margolin, Gennady (NIH/NICHD) [C]" <gennady.margolin at nih.gov> Cc: "bioc-devel at r-project.org" <bioc-devel at r-project.org> Subject: Re: [Bioc-devel] Question about org.Dr.eg.db package 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" "ENSEMBLPROT" "ENSEMBLTRANS" [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME" [11] "GO" "GOALL" "IPI" "ONTOLOGY" "ONTOLOGYALL" [16] "PATH" "PFAM" "PMID" "PROSITE" "REFSEQ" [21] "SYMBOL" "UNIGENE" "UNIPROT" "ZFIN"
On Thu, Aug 13, 2020 at 2:13 PM Margolin, Gennady (NIH/NICHD) [C] via Bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> wrote:
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 DB. Thank you, Gennady _______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.