Hello
I am trying to apply a function to each element of a GeneSetCollection object. I have a problem preserving the data class, if I use lapply(). Is using a for loop my only option?
Thanks for any help
-burak

Here's what I do:

> gsc
GeneSetCollection
  names: chr16q, chr5q23, ..., INOSITOL_OR_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITY (5452 total)
  unique identifiers: CMAR, USP10, ..., UCHL5IP (39655 total)
  types in collection:
    geneIdType: SymbolIdentifier (1 total)
    collectionType: BroadCollection (1 total)

> test1 = GeneSetCollection(gsc[[1]],gsc[[2]])
> test1
GeneSetCollection
  names: chr16q, chr5q23 (2 total)
  unique identifiers: CMAR, USP10, ..., LOC728586 (91 total)
  types in collection:
    geneIdType: SymbolIdentifier (1 total)
    collectionType: BroadCollection (1 total)

> lapply(test1,function(f) {geneIds(f) = "burak";return(f)})
[[1]]
setName: chr16q
geneIds: burak (total: 1)
geneIdType: Symbol
collectionType: Broad
  bcCategory: c1 (Positional)
  bcSubCategory:  NA
details: use 'details(object)'

[[2]]
setName: chr5q23
geneIds: burak (total: 1)
geneIdType: Symbol
collectionType: Broad
  bcCategory: c1 (Positional)
  bcSubCategory:  NA
details: use 'details(object)'

## returns a list

> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grDevices datasets  splines   graphics  stats     utils     tools
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_2.2.6  RSQLite_0.7-1       GSEABase_1.4.0
 [4] graph_1.20.0        annotate_1.20.0     xtable_1.5-4
 [7] AnnotationDbi_1.4.1 RMySQL_0.6-1        DBI_0.2-4
[10] simpleaffy_2.18.0   gcrma_2.14.1        matchprobes_1.14.0
[13] genefilter_1.22.0   survival_2.34-1     affy_1.20.0
[16] Biobase_2.2.0

loaded via a namespace (and not attached):
[1] affyio_1.10.1        cluster_1.11.11      preprocessCore_1.4.0
[4] XML_1.98-1


      
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