The GeneSetCollection class in the Bioconductor package GSEABase
extends 'list'
> library(GSEABase)
> showClass("GeneSetCollection")
Slots:
Name: .Data
Class: list
Extends:
Class "list", from data part
Class "vector", by class "list", distance 2
Class "AssayData", by class "list", distance 2
If I create an instance of this class and serialize it
> x <- GeneSetCollection(GeneSet("X"))
> x
GeneSetCollection
names: NA (1 total)
> save(x, file="/tmp/x.rda")
and then start a new R session and load the data object (without first
library(GSEABase)), the 'show' method is not added to the appropriate
method table.
> load("/tmp/x.Rda")
> x
Loading required package: GSEABase
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
An object of class "GeneSetCollection"
[[1]]
setName: NA
geneIds: X (total: 1)
geneIdType: Null
collectionType: Null
details: use 'details(object)'
Actually, the behavior is more complicate than appears; in a new R
session after loading /tmp/x.Rda, if I immediately do x[[1]] I get the
show,GeneSetCollection-method but not show,GeneSet-method.
Sorry for the somewhat obscure example.
Martin
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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