Thanks to all for tackling this so quickly. -steve
On Mon, Nov 23, 2015 at 6:59 AM, Jim Hester <james.f.hes...@gmail.com> wrote: > Panther has been updated to the new 1.03, which should resolve this issue. > Let us know if there are any further updates. > > On Fri, Nov 20, 2015 at 5:29 AM, Julius Müller <m...@jmuller.eu> wrote: > >> Dear Steve, >> >> thanks a lot for pointing out the error! The problem Martin described is >> exactly the problem addressed in PANTHER.db version 1.02. However the >> version available on bioconductor is not v1.02. >> The method type2col in PANTHER.db 1.02 should look like this: >> >> type2col <- function(x){ >> >> column_names <- >> c("family_id","goslim_id","ontology","uniprot_id","species","family_term","subfamily_term","class_id","class_term","go_id","go_term","component_go_id","component_term","evidence","evidence_type","confidence_code","entrez_id") >> names(column_names) <- .cols(x) >> column_names >> } >> >> >> What's puzzling to me is that there are unit tests included in the loading >> routine, so checking the version currently available on bioconductor should >> have choked executing PANTHER.db:::.test() >> I remember when I first uploaded the new version to Jim, I have send an >> old version by accident and then later on the correct version. This might >> have caused some confusion. >> Can somebody send me another aspera invite, then we can make sure that you >> have got the right version? >> >> Many thanks and apologies if this caused any troubles, >> Julius >> >> >> >> On 20/11/2015 09:46, Morgan, Martin wrote: >> >> From the head of >> >> >> PANTHER.db:::.keys >> >> function (x, keytype) >> { >> t2t <- .type2table(x) >> t2c <- .type2col(x) >> >> I wonder if many of the columns / keytypes are mislabeled, e.g., >> >> >> PANTHER.db:::.type2col(PANTHER.db) >> >> CLASS_ID CLASS_TERM COMPONENT_ID COMPONENT_TERM >> "family_id" "goslim_id" "ontology" "uniprot_id" >> CONFIDENCE_CODE ENTREZ EVIDENCE EVIDENCE_TYPE >> "species" "family_term" "subfamily_term" "class_id" >> FAMILY_ID FAMILY_TERM GOSLIM_ID GOSLIM_TERM >> "class_term" "go_id" "go_term" "component_go_id" >> PATHWAY_ID PATHWAY_TERM SPECIES SUBFAMILY_TERM >> "component_term" "evidence" "evidence_type" "confidence_code" >> UNIPROT >> "entrez_id" >> >> probably because columns() is used in .type2* but was changed at some point >> to return sorted values >> >> >> showMethods(PANTHER.db:::.type2col, includeDefs=TRUE) >> >> Function: .type2col (package PANTHER.db) >> x="PANTHER.db" >> function (x) >> { >> cls <- c("family_id", "goslim_id", "ontology", "uniprot_id", >> "species", "family_term", "subfamily_term", "class_id", >> "class_term", "go_id", "go_term", "component_go_id", >> "component_term", "evidence", "evidence_type", "confidence_code", >> "entrez_id") >> names(cls) <- columns(x) >> cls >> } >> >> >> columns >> >> nonstandardGenericFunction for "columns" defined from package "AnnotationDbi" >> >> function (x) >> { >> value <- standardGeneric("columns") >> sort(value) >> } >> >> >> selectMethod("columns", "PANTHER.db") >> >> Method Definition: >> >> function (x) >> { >> c("FAMILY_ID", "GOSLIM_ID", "GOSLIM_TERM", "UNIPROT", "SPECIES", >> "FAMILY_TERM", "SUBFAMILY_TERM", "CLASS_ID", "CLASS_TERM", >> "PATHWAY_ID", "PATHWAY_TERM", "COMPONENT_ID", "COMPONENT_TERM", >> "EVIDENCE", "EVIDENCE_TYPE", "CONFIDENCE_CODE", "ENTREZ") >> } >> >> Probably a better design is to define a package-global constant >> >> .TYPE2COLUMN = c(FAMILY_ID="family_id", GOSLIM_ID="goslim_id", ...) >> >> and implement columns,PANTHER.db-method as names(.TYPE2COLUMN) >> >> Martin Morgan >> ________________________________________ >> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Steve >> Lianoglou [lianoglou.st...@gene.com] >> Sent: Friday, November 20, 2015 4:24 AM >> To: bioc-devel@r-project.org >> Subject: [Bioc-devel] PANTHER.db GOSLIM_ID hosed? >> >> Hi all, >> >> I'm running the latest Bioc + PANTHER.db >> >> I think we've got the GOSLIM_TERM where the GOSLIM_ID should be: >> >> In the vignette, we have this: >> >> R> go_ids <- head(keys(PANTHER.db,keytype="GOSLIM_ID")) >> R> go_ids >> >> ## [1] "GO:0000003" "GO:0000165" "GO:0000166" "GO:0000228" >> "GO:0000375" "GO:0000398" >> >> But what we really get is: >> >> R> head(keys(PANTHER.db,keytype="GOSLIM_ID")) >> >> [1] "2-arachidonoylglycerol biosynthesis" >> [2] "5-Hydroxytryptamine biosynthesis" >> [3] "5-Hydroxytryptamine degredation" >> [4] "5HT1 type receptor mediated signaling pathway" >> >> R> packageVersion('PANTHER.db') >> [1] '1.0.2' >> >> Thanks, >> -steve >> >> _______________________________________________bioc-de...@r-project.org >> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> >> >> >> -- >> Julius Müller 1A All Saints Road OX3 7AU, Oxford United Kingdom Phone: +44 >> 750 828 0522 m...@jmuller.eu >> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Steve Lianoglou Computational Biologist Genentech _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel