[Bioc-devel] Problem with S4 method dispatch: method found for SummarizedExperiment, but not SingleCellExperiment
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Jan 9 20:31:16 CET 2025
Looks like a bug in the methods package to me.
The extends() relationship looks transitive, as it should be:
> extends("SingleCellExperiment", "SummarizedExperiment")
[1] TRUE
> is(new("SingleCellExperiment"), "ExpData")
[1] TRUE
> extends("SingleCellExperiment", "ExpData")
[1] TRUE
Also is() is doing the right thing as Helena pointed out:
> is(new("SingleCellExperiment"), "ExpData")
[1] TRUE
However, when using the single-arg form of extends() to list all the
ancestor classes, ExpData is no longer seen as an ancestor of
SingleCellExperiment:
> extends("SummarizedExperiment")
[1] "SummarizedExperiment" "RectangularData" "Vector"
[4] "ExpData" "Annotated" "vector_OR_Vector"
> extends("SingleCellExperiment")
[1] "SingleCellExperiment" "RangedSummarizedExperiment"
[3] "SummarizedExperiment" "RectangularData"
[5] "Vector" "Annotated"
[7] "vector_OR_Vector"
Same problem with selectSuperClasses(), which is an other way to list
all the ancestors of a given class:
> selectSuperClasses("SummarizedExperiment", directOnly=FALSE)
[1] "RectangularData" "Vector" "ExpData" "Annotated"
[5] "vector_OR_Vector"
> selectSuperClasses("SingleCellExperiment", directOnly=FALSE)
[1] "RangedSummarizedExperiment" "SummarizedExperiment"
[3] "RectangularData" "Vector"
[5] "Annotated" "vector_OR_Vector"
And same problem when trying to retrieve this list directly from the
'contains' slot of the class definitions:
> names(getClass("SummarizedExperiment")@contains)
[1] "RectangularData" "Vector" "ExpData" "Annotated"
[5] "vector_OR_Vector"
> names(getClass("RangedSummarizedExperiment")@contains)
[1] "SummarizedExperiment" "RectangularData" "Vector"
[4] "ExpData" "Annotated" "vector_OR_Vector"
> names(getClass("SingleCellExperiment")@contains)
[1] "RangedSummarizedExperiment" "SummarizedExperiment"
[3] "RectangularData" "Vector"
[5] "Annotated" "vector_OR_Vector"
Any volunteer to report this to the methods maintainer? (via the R bug
tracker)
Anyways, not sure exactly what methods you're planning to implement for
ExpData derivatives. Have you considered doing something like this instead:
.check_expdata <- function(expdata)
{
ok <- is.matrix(expdata) ||
is(expdata, "dgCMatrix") ||
is(expdata, "ExpressionSet") ||
is(expdata, "SummarizedExperiment")
if (!ok) stop("'expdata' must be a matrix or dgCMatrix or ",
"ExpressionSet or SummarizedExperiment derivative")
}
foo <- function(expdata)
{
.check_expdata(expdata)
...
...
}
Personally I find that using a union and method dispatch for this is a
little bit overkill.
Best,
H.
On 1/8/25 05:35, Helena L. Crowell wrote:
> Ui, my bad, messed up my environment… Indeed, I think what you had in mind doesn’t work. My guess is that the class union is “strict” in that method dispatch doesn’t just propagate to classes that inherit from what’s in the union.
>
> Anything against something like … which should definitely work (I think):
>
> setClassUnion("ExpData", c(
> "matrix", "dgCMatrix", "ExpressionSet",
> "SingleCellExperiment", "SummarizedExperiment”))
>
> What’s really weird imo is that is(se, "ExpData”) and is(sce, "ExpData”) both return TRUE, but still the SCE method can’t be found?
> Maybe someone else has more insights, sorry!!
>
>> On Jan 8, 2025, at 14:11, Axel Klenk <axel.klenk using gmail.com> wrote:
>>
>> Hi Helena,
>>
>> thanks for your reply. Unfortunately it doesn't work for me -- when
>> copy+paste'ing your code
>> the error now occurs for SummarizedExperiment (transcript below,
>> including session info
>> that I had forgotten yesterday).
>>
>> In the current version of GSVA the class union contains all of SE, SCE
>> and SPE and we
>> still need to define all methods for all of them which doesn't feel
>> right... but I must be doing
>> something wrong.
>>
>> Any ideas?
>>
>> Cheers,
>>
>> - axel
>>
>>
>>> library("Matrix")
>>> library("Biobase")
>> Loading required package: BiocGenerics
>>
>> Attaching package: 'BiocGenerics'
>>
>> The following objects are masked from 'package:stats':
>>
>> IQR, mad, sd, var, xtabs
>>
>> The following objects are masked from 'package:base':
>>
>> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>> Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
>> table, tapply, union, unique, unsplit, which.max, which.min
>>
>> Welcome to Bioconductor
>>
>> Vignettes contain introductory material; view with
>> 'browseVignettes()'. To cite Bioconductor, see
>> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>>
>>> library("SummarizedExperiment")
>> Loading required package: MatrixGenerics
>> Loading required package: matrixStats
>>
>> Attaching package: 'matrixStats'
>>
>> The following objects are masked from 'package:Biobase':
>>
>> anyMissing, rowMedians
>>
>>
>> Attaching package: 'MatrixGenerics'
>>
>> The following objects are masked from 'package:matrixStats':
>>
>> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
>> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
>> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
>> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
>> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
>> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
>> colWeightedMeans, colWeightedMedians, colWeightedSds,
>> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
>> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
>> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
>> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
>> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
>> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
>> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
>> rowWeightedSds, rowWeightedVars
>>
>> The following object is masked from 'package:Biobase':
>>
>> rowMedians
>>
>> Loading required package: GenomicRanges
>> Loading required package: stats4
>> Loading required package: S4Vectors
>>
>> Attaching package: 'S4Vectors'
>>
>> The following objects are masked from 'package:Matrix':
>>
>> expand, unname
>>
>> The following object is masked from 'package:utils':
>>
>> findMatches
>>
>> The following objects are masked from 'package:base':
>>
>> expand.grid, I, unname
>>
>> Loading required package: IRanges
>> Loading required package: GenomeInfoDb
>>> library("SingleCellExperiment")
>>> setClassUnion("ExpData", c("matrix", "dgCMatrix",
>> + "ExpressionSet", "SingleCellExperiment"))
>>> setGeneric("expShow", \(.) standardGeneric("expShow"))
>> [1] "expShow"
>>> setMethod("expShow", "ExpData", \(.) show(.))
>>> 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)
>>> sce <- SingleCellExperiment(y)
>>> expShow(se)
>> Error: unable to find an inherited method for function 'expShow' for
>> signature '. = "SummarizedExperiment"'
>>> expShow(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):
>>>
>>>
>>> sessionInfo()
>> R version 4.4.2 (2024-10-31)
>> Platform: x86_64-pc-linux-gnu
>> Running under: Ubuntu 20.04.6 LTS
>>
>> Matrix products: default
>> BLAS: /home/axel/R/local/R-4.4.2/lib/libRblas.so
>> LAPACK: /home/axel/R/local/R-4.4.2/lib/libRlapack.so; LAPACK version 3.12.0
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>>
>> time zone: Europe/Madrid
>> tzcode source: system (glibc)
>>
>> attached base packages:
>> [1] stats4 stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] SingleCellExperiment_1.28.1 SummarizedExperiment_1.36.0
>> [3] GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
>> [5] IRanges_2.40.1 S4Vectors_0.44.0
>> [7] MatrixGenerics_1.18.0 matrixStats_1.5.0
>> [9] Biobase_2.66.0 BiocGenerics_0.52.0
>> [11] Matrix_1.7-1
>>
>> loaded via a namespace (and not attached):
>> [1] R6_2.5.1 SparseArray_1.6.0 zlibbioc_1.52.0
>> [4] lattice_0.22-6 abind_1.4-8 GenomeInfoDbData_1.2.13
>> [7] S4Arrays_1.6.0 XVector_0.46.0 UCSC.utils_1.2.0
>> [10] fortunes_1.5-4 grid_4.4.2 DelayedArray_0.32.0
>> [13] compiler_4.4.2 httr_1.4.7 tools_4.4.2
>> [16] crayon_1.5.3 jsonlite_1.8.9
>>
>> Am Mi., 8. Jan. 2025 um 13:41 Uhr schrieb Helena L. Crowell <helena using crowell.eu>:
>>> SCE inherits from SE, but not vice versa. So setting the class union on SCE (not SE) will do the trick. Briefly, Anything defined on an SCE will work upstream (SE), but anything defined on SE will not work downstream (SPE, SCE).
>>>
>>> ***
>>>
>>> This works:
>>>
>>> library("Matrix")
>>> library("Biobase")
>>> library("SummarizedExperiment")
>>> library("SingleCellExperiment")
>>>
>>> setClassUnion("ExpData", c("matrix", "dgCMatrix",
>>> "ExpressionSet", "SingleCellExperiment"))
>>>
>>> setGeneric("expShow", \(.) standardGeneric("expShow"))
>>> setMethod("expShow", "ExpData", \(.) show(.))
>>>
>>> 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)
>>> sce <- SingleCellExperiment(y)
>>>
>>> expShow(se)
>>> expShow(sce)
>>>
>>>> On Jan 7, 2025, at 21:33, Axel Klenk <axel.klenk using gmail.com> wrote:
>>>>
>>>> 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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org mailing list
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>>>>
> _______________________________________________
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.github using gmail.com
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