[Bioc-devel] PANTHER.db GOSLIM_ID hosed?
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-bounces at r-project.org] on behalf of Steve Lianoglou [lianoglou.steve at gene.com]
Sent: Friday, November 20, 2015 4:24 AM
To: bioc-devel at 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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