Dear Community, dear S4 Experts,
in the GSVA package I want to use an S4 class union as a superclass
for all supported data containers and S4 methods
defined for this superclass, rather than for each subclass, where a
class-specific implementation is not necessary. In particular
I want to avoid having to implement individual methods for all current
(and possibly, future) subclasses of SummarizedExperiment
for common operations like accessing assay names and dimensions, assay
data, etc.
As you can see from the example code and output below, this works as
expected for SummarizedExperiment objects but not
for its subclasses such as SingleCellExperiment or SpatialExperiment
(if SummarizedExperiment is part of the class union and
the others are not). In the latter case the result is "Error: unable
to find an inherited method for function ..." (please see below).
I'd be very grateful if someone with more S4 expertise than myself
could please let me know if and how this can be solved -- or
if the whole thing is not a good idea at all. ;-)
Thanks a lot,
- axel
### define a class union as a common superclass
library("Matrix")
library("Biobase")
library("SummarizedExperiment")
library("SingleCellExperiment")
## [package startup messages omitted]
setClassUnion("ExpData",
c("matrix", "dgCMatrix", "ExpressionSet", "SummarizedExperiment"))
### ... and an example method for the superclass
setGeneric("expShow", function(object) standardGeneric("expShow"))
setMethod("expShow",
signature=signature(object="ExpData"),
function(object) {
show(object)
})
### generate some example data and test the method:
p <- 10
n <- 30
y <- matrix(rnorm(n*p), nrow=p, ncol=n,
dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, sep="")))
se <- SummarizedExperiment(y)
show(se)
## class: SummarizedExperiment
## dim: 10 30
## metadata(0):
## assays(1): ''
## rownames(10): g1 g2 ... g9 g10
## rowData names(0):
## colnames(30): s1 s2 ... s29 s30
## colData names(0):
expShow(se)
## class: SummarizedExperiment
## dim: 10 30
## metadata(0):
## assays(1): ''
## rownames(10): g1 g2 ... g9 g10
## rowData names(0):
## colnames(30): s1 s2 ... s29 s30
## colData names(0):
sce <- SingleCellExperiment(y)
show(sce)
## class: SingleCellExperiment
## dim: 10 30
## metadata(0):
## assays(1): ''
## rownames(10): g1 g2 ... g9 g10
## rowData names(0):
## colnames(30): s1 s2 ... s29 s30
## colData names(0):
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
expShow(sce)
## Error: unable to find an inherited method for function 'expShow'
for signature 'object = "SingleCellExperiment"'
### ### ###
## we can define a new subclass of SummarizedExperiment in the global
environment that works -- as
## long as it is not coerced to SingleCellExperiment
setClass("expA",
contains="RangedSummarizedExperiment")
ea <- new("expA")
show(ea)
## An object of class "expA"
## Slot "rowRanges":
## GRanges object with 0 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## -------
## seqinfo: no sequences
##
## Slot "colData":
## DataFrame with 0 rows and 0 columns
##
## Slot "assays":
## NULL
##
## Slot "NAMES":
## NULL
##
## Slot "elementMetadata":
## DataFrame with 0 rows and 0 columns
##
## Slot "metadata":
## list()
expShow(ea)
## class: SummarizedExperiment
## dim: 0 0
## metadata(0):
## assays(0):
## rownames: NULL
## rowData names(0):
## colnames: NULL
## colData names(0):
scea <- as(ea, "SingleCellExperiment")
show(scea)
## class: SingleCellExperiment
## dim: 0 0
## metadata(0):
## assays(0):
## rownames: NULL
## rowData names(0):
## colnames: NULL
## colData names(0):
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
expShow(scea)
## Error: unable to find an inherited method for function 'expShow'
for signature 'object = "SingleCellExperiment"'
### ### ### ### ###
## as shown below, SummarizedExperiment and ExpData "know" about their
inheritance relation but
## SingleCellExperiment does not...
getClass("SummarizedExperiment")
## Class "SummarizedExperiment" [package "SummarizedExperiment"]
##
## Slots:
##
## Name: colData assays NAMES
elementMetadata metadata
## Class: DataFrame Assays_OR_NULL character_OR_NULL
DataFrame list
##
## Extends:
## Class "RectangularData", directly
## Class "Vector", directly
## Class "ExpData", directly
## Class "Annotated", by class "Vector", distance 2
## Class "vector_OR_Vector", by class "Vector", distance 2
##
## Known Subclasses:
## Class "RangedSummarizedExperiment", directly, with explicit coerce
getClass("ExpData")
## Extended class definition ( "ClassUnionRepresentation" )
## Virtual Class "ExpData" [in ".GlobalEnv"]
##
## No Slots, prototype of class "matrix"
##
## Known Subclasses:
## Class "matrix", directly
## Class "dgCMatrix", directly
## Class "ExpressionSet", directly
## Class "SummarizedExperiment", directly
## Class "mts", by class "matrix", distance 2
## Class "RangedSummarizedExperiment", by class
"SummarizedExperiment", distance 2, with explicit coerce
getClass("SingleCellExperiment")
## Class "SingleCellExperiment" [package "SingleCellExperiment"]
##
## Slots:
##
## Name: int_elementMetadata int_colData
int_metadata
## Class: DataFrame DataFrame
list
##
## Name: rowRanges colData
assays
## Class: GenomicRanges_OR_GRangesList DataFrame
Assays_OR_NULL
##
## Name: NAMES elementMetadata
metadata
## Class: character_OR_NULL DataFrame
list
##
## Extends:
## Class "RangedSummarizedExperiment", directly
## Class "SummarizedExperiment", by class
"RangedSummarizedExperiment", distance 2
## Class "RectangularData", by class "RangedSummarizedExperiment", distance 3
## Class "Vector", by class "RangedSummarizedExperiment", distance 3
## Class "Annotated", by class "RangedSummarizedExperiment", distance 4
## Class "vector_OR_Vector", by class "RangedSummarizedExperiment", distance 4
### ### ### ### ###
getClass("SummarizedExperiment")
## Class "SummarizedExperiment" [package "SummarizedExperiment"]
##
## Slots:
##
## Name: colData assays NAMES
elementMetadata metadata
## Class: DataFrame Assays_OR_NULL character_OR_NULL
DataFrame list
##
## Extends:
## Class "RectangularData", directly
## Class "Vector", directly
## Class "ExpData", directly
## Class "Annotated", by class "Vector", distance 2
## Class "vector_OR_Vector", by class "Vector", distance 2
##
## Known Subclasses:
## Class "RangedSummarizedExperiment", directly, with explicit coerce
## Class "expA", by class "RangedSummarizedExperiment", distance 2,
with explicit coerce
getClass("expA")
## Class "expA" [in ".GlobalEnv"]
##
## Slots:
##
## Name: rowRanges colData
assays
## Class: GenomicRanges_OR_GRangesList DataFrame
Assays_OR_NULL
##
## Name: NAMES elementMetadata
metadata
## Class: character_OR_NULL DataFrame
list
##
## Extends:
## Class "RangedSummarizedExperiment", directly
## Class "SummarizedExperiment", by class
"RangedSummarizedExperiment", distance 2, with explicit coerce
## Class "RectangularData", by class "RangedSummarizedExperiment", distance 3
## Class "Vector", by class "RangedSummarizedExperiment", distance 3
## Class "ExpData", by class "RangedSummarizedExperiment", distance 3,
with explicit coerce
## Class "Annotated", by class "RangedSummarizedExperiment", distance 4
## Class "vector_OR_Vector", by class "RangedSummarizedExperiment", distance 4
getClass("SingleCellExperiment")
## Class "SingleCellExperiment" [package "SingleCellExperiment"]
##
## Slots:
##
## Name: int_elementMetadata int_colData
int_metadata
## Class: DataFrame DataFrame
list
##
## Name: rowRanges colData
assays
## Class: GenomicRanges_OR_GRangesList DataFrame
Assays_OR_NULL
##
## Name: NAMES elementMetadata
metadata
## Class: character_OR_NULL DataFrame
list
##
## Extends:
## Class "RangedSummarizedExperiment", directly
## Class "SummarizedExperiment", by class
"RangedSummarizedExperiment", distance 2
## Class "RectangularData", by class "RangedSummarizedExperiment", distance 3
## Class "Vector", by class "RangedSummarizedExperiment", distance 3
## Class "Annotated", by class "RangedSummarizedExperiment", distance 4
## Class "vector_OR_Vector", by class "RangedSummarizedExperiment", distance 4
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