Hi Martin and all,
> In principle it should be reproducible with only base R (incl
> methods package), not involving your given extra packages;
> just using functions setClassUnion(), ... etc from methods.
>
> Is that possible?
Yes, it is -- but I found that in order to reproduce the issue I need
to mimic the "original" constellation
where class A and its subclass C are defined in some example package
expkg and D, a subclass of C
is defined in a dependent package depkg. Then a method defined for a
class union U of class A and
some other class B will be found for an object of class C (same
package as A), but not one of class D
(different package)... I have prepared two packages expkg and depkg
on my GitHub to demonstrate
this as follows:
if(!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github(c("axelklenk/expkg", "axelklenk/depkg"))
library("expkg")
setClass("B")
setClassUnion("U", c("A", "B"))
setGeneric("Umethod", function(x) standardGeneric("Umethod"))
setMethod("Umethod", signature="U", function(x) cat("Found Umethod!\n"))
o <- new("C")
Umethod(o) ## it works!!
library("depkg")
p <- new("D")
Umethod(p)
## Error: unable to find an inherited method for function 'Umethod'
for signature 'x = "D"'
The packages contain nothing but the necessary setClass() and their
respective NAMESPACE
files are pretty simple. For expkg, the package defining superclasses A and C:
exportClasses(A)
exportClasses(C)
import(methods)
and for depkg, the package defining subclass D
exportClasses(D)
import(methods)
importClassesFrom(expkg,A)
importClassesFrom(expkg,C)
I have studied WRE 1.5[.6] and added "Depends: methods¨ to the
packages' DESCRIPTION files and
"import(methods)" to their NAMESPACE files but that didn't seem to
make a difference. Otherwise I didn't
find any hints in WRE.
Ah, and after running the code above, the inheritance relation between
U and C is "known" as well as
between A and D, but not between U and D:
> getClass("C")
Class "C" [package "expkg"]
No Slots, prototype of class "S4"
Extends:
Class "A", directly
Class "U", by class "A", distance 2
> getClass("D")
Class "D" [package "depkg"]
No Slots, prototype of class "S4"
Extends:
Class "C", directly
Class "A", by class "C", distance 2
> getClass("U")
Extended class definition ( "ClassUnionRepresentation" )
Virtual Class "U" [in ".GlobalEnv"]
No Slots, prototype of class "C"
Known Subclasses:
Class "A", directly
Class "B", directly
Class "C", by class "A", distance 2
Now, does that look like a bug in the methods package or rather like
'some "unhappy coincidence" in how the involved packages interact there'?
I have no idea how to tell -- and therefore will follow this advice:
> Otherwise, yes, do as you are advised, i.e. -->
> https://www.r-project.org/bugs.html
> and apply for an R bugzilla account.
Thanks to all for your help so far and any additional advice,
- axel
Am Mi., 15. Jan. 2025 um 09:08 Uhr schrieb Martin Maechler
<maech...@stat.math.ethz.ch>:
>
> >>>>> Axel Klenk
> >>>>> on Sat, 11 Jan 2025 01:16:49 +0100 writes:
>
> > Hi Hervé, Kasper, Helena and all,
> > and thanks a lot for your replies!
>
> > First of all, if this is a bug in the methods package, I'd of course
> > volunteer to report it -- sounds like a great learning opportunity
> > for the New Year. ;-)
>
> As an R corer with special interest in S4/ methods, I had wanted to chime in
> earlier:
> Yes, _if this is a bug in the methods package_
>
> In principle it should be reproducible with only base R (incl
> methods package), not involving your given extra packages;
> just using functions setClassUnion(), ... etc from methods.
>
> Is that possible?
>
> Of course, it might be that it is related to the use of
>
> ImportClassesFrom(),
> ImportMethodsFrom(),
> ExportClasses()
> ...
>
> directives in the involved packages' NAMESPACE files,
> and some "unhappy coincidence" in how the involved packages
> interact there ..
> but probably Hervé or you have already looked into these.
>
> Otherwise, yes, do as you are advised, i.e. -->
> https://www.r-project.org/bugs.html
> and apply for an R bugzilla account.
>
> Best,
> Martin
>
>
> > In my original message I tried to focus on the error and provided only
> > the code necessary to reproduce it but of course I'm happy
> > to provide more background and receive advice on design and
> maintainability.
>
> > The reason for class unions was the need to store any user-provided
> > data container in a slot of GSVA's parameter objects when
> > those were introduced. (Actually there is one for data
> > matrices/containers and another one for gene sets in lists or
> > GSEABase::GeneSetCollection.) As you seem to be a bit reluctant to
> > use class unions, is there a good way to avoid them as
> > the slot class in this case?
>
> > Once the class union existed, methods on the union were added to avoid
> > long functions with unwieldy if/else constructs, as the
> > number of supported containers is growing. However, so far there are
> > only two actual use cases for methods on class unions:
> > (1) the (containing) parameter object's show() method that includes
> > output from show() methods of the (contained) data objects,
> > with more specialized methods only required for matrix and dgCMatrix
> > that otherwise show() all of their content, and
> > (2) some method for extracting a matrix-like data object from a data
> > container -- assay() for SummarizedExperiment and derivatives,
> > exprs() for ExpressionSet, the object itself for matrix/dgCMatrix.
>
> > So, we are actually starting from the class unions rather than the
> > methods that could be replaced the way Hervé suggested.
> > The methods are just where the error message happened to appear and I
> > was not sure if this was caused by a bug or not expected
> > to work at all or a known issue requiring some special measures or ...
>
> > By the way, in the meantime we have been experimenting with the mock
> > example below -- which works as expected?!?
>
> > setClass("A") ## this would be like 'dgCMatrix'
> > setClass("B") ## this would be like 'SummarizedExperiment'
> > setClass("C", contains="B") ## this would be like 'SingleCellExperiment'
> > setClassUnion("U", c("A", "B"))
> > setGeneric("Umethod", function(x) standardGeneric("Umethod"))
> > setMethod("Umethod", signature="U", function(x) cat("Umethod!\n"))
> > o <- new("C")
> > Umethod(o) ## it works!!
>
> > Thanks in advance for your support and suggestions,
>
> > - axel
>
>
> > Am Fr., 10. Jan. 2025 um 18:17 Uhr schrieb Kasper Daniel Hansen
> > <kasperdanielhan...@gmail.com>:
> >>
> >> In my experience, class unions are hard to work with and quickly get
> out of hand. I don't really understand what you actually want to do, beyond
> defining a class union. My impression is that your main goal is to write
> simplified code. I could be wrong, but I doubt class unions is the best way
> to solve your problem. What you really need is that these classes share a
> common API in that you can do stuff like
> >> assay()
> >> on them. Either this common API already exists or it does not. It it
> already exists, there is - as far as I can tell - no gains from the class
> union. If it does not exist, you still need to write class specific code to
> get the API working.
> >>
> >> Like Herve, I suggest not starting with a method. I find that too many
> developers are too quick to reach for methods.
> >>
> >> We might be able to give you more useful feedback and help if you can
> tell us more precisely what you want to do.
> >>
> >> Best,
> >> Kasper
> >>
> >>
> >> On Thu, Jan 9, 2025 at 2:38 PM Hervé Pagès
> <hpages.on.git...@gmail.com> wrote:
> >>>
> >>> 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.kl...@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
> <hel...@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.kl...@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@r-project.org mailing list
> >>> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> >>>>
> >>> > _______________________________________________
> >>> > Bioc-devel@r-project.org mailing list
> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>> --
> >>> Hervé Pagès
> >>>
> >>> Bioconductor Core Team
> >>> hpages.on.git...@gmail.com
> >>>
> >>> _______________________________________________
> >>> Bioc-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >>
> >> --
> >> Best,
> >> Kasper
>
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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