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

thanks Vincent,

what you suggest fixes the situation temporarily and hopefully, as
Martin said in his message before, this can have a more generic
solution.

you suggestion makes me think that, in fact, it could be of general
interest to add a *ENTREZID (identity) map for every entrez-based
organism-level annotation package. i think this could be useful in every
situation in which one would like to programmatically retrieve the
entrez id of a feature using any annotation package without knowing
whether the feature is already an entrez id.

robert.


On Mon, 2012-02-27 at 07:45 -0500, Vincent Carey wrote:

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.