In PeteHaitch/cometh: Analyse, manage and visualise co-methylation data.

Motivation

The [ method is not working as expected for my simple class that extends the SummarizedExperiment class.

Example

This example shows the unexpected (to me) behaviour.

MyClass definition

Define MyClass, basically a SummarizedExperiment with an extraSlot, which is a numeric vector of the same length as the number of rows in the rowData:

require(GenomicRanges)
.MyClass <- setClass("MyClass", representation(extraSlot = "vector"), contains = "SummarizedExperiment")

MyClass constructor

MyClass <- function(assays, gr, extraSlot){
  se <- SummarizedExperiment(assays = assays, rowData = gr)
  mc <- .MyClass(se, extraSlot = extraSlot)
  mc
}

[ method definition for MyClass

Define the [ method for MyClass objects. Should basically do the same thing as [ for a SummarizedExperiment but also subset the extraSlot:

setMethod("[", c("MyClass", "ANY", "missing"),
          function(x, i, j, ..., drop = FALSE)
          {
            if (missing(i) && missing(j)){
              return(x)
            }
            if (missing(i)){
              i <- seq_len(nrow(x))
            }
            if (missing(j)){
              j <- seq_len(ncol(x))
            }
            initialize(x, as(x, "SummarizedExperiment")[i, j, ..., drop = drop], extraSlot = x@extraSlot[i])
            })

Example data

nrows <- 20
ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colnames(counts) <- letters[1:6]
gr <- GRanges('chr1', IRanges(floor(runif(nrows, 1e5, 1e6)), width=100))
extraSlot <- runif(n = length(gr))

ex <- MyClass(assays = SimpleList(counts), gr = gr, extraSlot = extraSlot)
ex
slotNames(ex)
ex@extraSlot

Testing the [ method for MyClass objects

As expected, the following contains 10 elements:

ex[1:10, ]@extraSlot

As unexpected, the following contains 20 elements. Why?

ex[1:10, 2]@extraSlot

As unexpected, the following contains 10 elements. Why? This is the exact same code as the final line of the [ method definition:

initialize(ex, as(ex, "SummarizedExperiment")[1:10, 2, drop = FALSE], extraSlot = ex@extraSlot[1:10])@extraSlot

Summary

I never got to the bottom of this. I didn't post a question to the Bioconductor mailing lists. MyClass was a simplified version of an earlier incarnation the CoMeth class. When I changed the definition of the CoMeth class[^cometh_class_definition], I got the intended subsetting behaviour of the [ method "for free" via inheritance. Therefore, this was no longer a problem for the cometh package, although it would be good to understand the behaviour in the example.

[^cometh_class_definition]: The CoMeth class definition changed to use the MTuples class, which extends the GRanges class, as the rowData, rather than the GRanges class itself. Effectively, the extraPos information is stored in the MTuples object and preserved in subsetting by use of the GenomicRanges:::extraColumnSlotNames function (see class definition of MTuples in R/AllClasses.R and the vignette Creating MTuples and CoMeth classes).

Session info

sessionInfo()

PeteHaitch/cometh documentation built on May 8, 2019, 1:32 a.m.