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-devel] PANTHER.db GOSLIM_ID hosed?
5 messages · Steve Lianoglou, Martin Morgan, Julius Müller +1 more
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
_______________________________________________
Bioc-devel at r-project.org mailing list
https://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 M?ller 1A All Saints Road OX3 7AU, Oxford United Kingdom Phone: +44 750 828 0522 mail at jmuller.eu <mailto:mail at jmuller.eu> [[alternative HTML version deleted]]
3 days later
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 M?ller <mail at 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-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
_______________________________________________Bioc-devel at 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 M?ller 1A All Saints Road OX3 7AU, Oxford United Kingdom Phone: +44
750 828 0522 mail at jmuller.eu
Thanks to all for tackling this so quickly. -steve
On Mon, Nov 23, 2015 at 6:59 AM, Jim Hester <james.f.hester at gmail.com> wrote:
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 M?ller <mail at 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-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
_______________________________________________Bioc-devel at 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 M?ller 1A All Saints Road OX3 7AU, Oxford United Kingdom Phone: +44
750 828 0522 mail at jmuller.eu
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Steve Lianoglou Computational Biologist Genentech