[Bioc-devel] idempotent identifier mapping with GSEABase::mapIdentifiers()

I have run into a very similar situation.  Ultimately a uniformization of
the annotation API will be called for.
I wonder if a global short-term fixup would get you through this situation?

org.Hs.egENTREZID = new.env(hash=TRUE)
k = mappedkeys(org.Hs.egENSEMBL)  # or any other good source of all keys
for (i in 1:length(k)) assign(k[i], k[i], org.Hs.egENTREZID)
get("1000", org.Hs.egENTREZID)

[1] "1000"


On Mon, Feb 27, 2012 at 6:25 AM, Robert Castelo<robert.castelo at upf.edu>wrote:

hi,

i collaborate mantaining the packages GSVA and GSVAdata and i have a
question about the function mapIdentifiers() from the GSEABase package
which i'm going to illustrate through an example.


1. let's build first an ExpressionSet object whose annotation slot is
going to point to the human organism-level annotation pacakge
org.Hs.eg.db:

library(Biobase)
library(org.Hs.eg.db)

mapped_genes<- mappedkeys(org.Hs.egSYMBOL)

exp<- matrix(rnorm(1000), nrow=100,
              dimnames=list(mapped_genes[1:100],
                            paste("sample", 1:10, sep="")))
eset<- new("ExpressionSet", exprs=exp, annotation="org.Hs.eg.db")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 100 features, 10 samples
  element names: exprs
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation: org.Hs.eg.db

2. now i'm going to load the Broad gene sets stored as a
GeneSetCollection object in the experimental data package GSVAdata:

library(GSVAdata)
data(c2BroadSets)
c2BroadSets
GeneSetCollection
  names: NAKAMURA_CANCER_MICROENVIRONMENT_UP,
NAKAMURA_CANCER_MICROENVIRONMENT_DN, ...,
ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY (3272 total)
  unique identifiers: 5167, 100288400, ..., 57191 (29340 total)
  types in collection:
    geneIdType: EntrezIdentifier (1 total)
    collectionType: BroadCollection (1 total)


3. finally, i'd like to obtain a new GeneSetCollection object whose
identifiers have been mapped between the two classes of identifiers in
the GeneSetCollection and the ExpressionSet objects.

in this case both objects actually work with the same class of
identifiers (Entrez), so in fact i don't need to do that but this
operation forms part of a piece of code in the package GSVA which i'd
like it to work regardless of the kind of annotation package referred to
in the ExpressionSet object. i had expected that the function
mapIdentifiers() would have some kind of idempotent behavior, but i get
the following error:

gsc<- mapIdentifiers(c2BroadSets,
                      AnnotationIdentifier(annotation(eset)))
Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose
= verbose)) :
  error in evaluating the argument 'object' in selecting a method for
function 'GeneSetCollection': Error in get(mapName, envir = pkgEnv,
inherits = FALSE) :
  object 'org.Hs.egENTREZID' not found


which does not occur if the feature names and annotation of the
ExpressionSet corresponds to a classical affy chip (e.g. "hgu95av2").

i built the object c2BroadSets in the experiment data package GSVAdata
by importing the entire xml file from the Broad sets so, i guess it
could be also possible that i did something wrong when i built this
'c2BroadSets' object and there's no problem, bug or lacking feature in
mapIdentifiers().

i look forward to your diagnostic and suggestions in any of these
possible directions.


thanks,
robert.

	[[alternative HTML version deleted]]

I have run into a very similar situation.  Ultimately a uniformization
of the annotation API will be called for.
I wonder if a global short-term fixup would get you through this
situation?

org.Hs.egENTREZID = new.env(hash=TRUE)
k = mappedkeys(org.Hs.egENSEMBL)  # or any other good source of all

keys

for (i in 1:length(k)) assign(k[i], k[i], org.Hs.egENTREZID)
get("1000", org.Hs.egENTREZID)

[1] "1000"


On Mon, Feb 27, 2012 at 6:25 AM, Robert Castelo
<robert.castelo at upf.edu> wrote:
        hi,
        
        i collaborate mantaining the packages GSVA and GSVAdata and i
        have a
        question about the function mapIdentifiers() from the GSEABase
        package
        which i'm going to illustrate through an example.
        
        
        1. let's build first an ExpressionSet object whose annotation
        slot is
        going to point to the human organism-level annotation pacakge
        org.Hs.eg.db:
        
        library(Biobase)
        library(org.Hs.eg.db)
        
        mapped_genes <- mappedkeys(org.Hs.egSYMBOL)
        
        exp <- matrix(rnorm(1000), nrow=100,
                     dimnames=list(mapped_genes[1:100],
                                   paste("sample", 1:10, sep="")))
        eset <- new("ExpressionSet", exprs=exp,
        annotation="org.Hs.eg.db")
        ExpressionSet (storageMode: lockedEnvironment)
        assayData: 100 features, 10 samples
         element names: exprs
        protocolData: none
        phenoData: none
        featureData: none
        experimentData: use 'experimentData(object)'
        Annotation: org.Hs.eg.db
        
        2. now i'm going to load the Broad gene sets stored as a
        GeneSetCollection object in the experimental data package
        GSVAdata:
        
        library(GSVAdata)
        data(c2BroadSets)
        c2BroadSets
        GeneSetCollection
         names: NAKAMURA_CANCER_MICROENVIRONMENT_UP,
        NAKAMURA_CANCER_MICROENVIRONMENT_DN, ...,
        ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY (3272 total)
         unique identifiers: 5167, 100288400, ..., 57191 (29340 total)
         types in collection:
           geneIdType: EntrezIdentifier (1 total)
           collectionType: BroadCollection (1 total)
        
        
        3. finally, i'd like to obtain a new GeneSetCollection object
        whose
        identifiers have been mapped between the two classes of
        identifiers in
        the GeneSetCollection and the ExpressionSet objects.
        
        in this case both objects actually work with the same class of
        identifiers (Entrez), so in fact i don't need to do that but
        this
        operation forms part of a piece of code in the package GSVA
        which i'd
        like it to work regardless of the kind of annotation package
        referred to
        in the ExpressionSet object. i had expected that the function
        mapIdentifiers() would have some kind of idempotent behavior,
        but i get
        the following error:
        
        gsc <- mapIdentifiers(c2BroadSets,
                             AnnotationIdentifier(annotation(eset)))
        Error in GeneSetCollection(lapply(what, mapIdentifiers,
        to, ..., verbose
        = verbose)) :
         error in evaluating the argument 'object' in selecting a
        method for
        function 'GeneSetCollection': Error in get(mapName, envir =
        pkgEnv,
        inherits = FALSE) :
         object 'org.Hs.egENTREZID' not found
        
        
        which does not occur if the feature names and annotation of
        the
        ExpressionSet corresponds to a classical affy chip (e.g.
        "hgu95av2").
        
        i built the object c2BroadSets in the experiment data package
        GSVAdata
        by importing the entire xml file from the Broad sets so, i
        guess it
        could be also possible that i did something wrong when i built
        this
        'c2BroadSets' object and there's no problem, bug or lacking
        feature in
        mapIdentifiers().
        
        i look forward to your diagnostic and suggestions in any of
        these
        possible directions.
        
        
        thanks,
        robert.