>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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