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
>
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--
Julius M�ller
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