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
