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