Subsetting with "missing" arguments

[allisonvuong]

Hi,

Matrix subsetting in base R supports "missing" subsetting arguments, but it seems the DelayedMatrix may not.

For example,

m <- matrix(runif(300000), nrow=10000, ncol=30)
M <- DelayedArray(m)

foo <- function(object, i, j) {
    object[i, j]
}

foo(m, j=!logical(ncol(m)))
foo(M, j=!logical(ncol(M)))

Is it possible to support this? I think packages like limma::subsetListOfArrays rely on such subsetting support for subsetting its EList objects.

Best,
Allison

[LTLA]

This seems to be an issue caused by S4 dispatch. You will see the same effect with sparse matrices:

library(Matrix)
n <- rsparsematrix(nrow=10000, ncol=30, density=0.1)
foo(n, j=!logical(ncol(n)))
## Error in object[i, j] : argument "i" is missing, with no default

My guess is that the S4 dispatch mechanism needs to know the class of i to choose an appropriate method... and i doesn't exist, leading to the observed error. While S4 dispatch does support missing arguments, it seems that only immediate missingness is supported and it is not propagated from symbols, for example:

library(SingleCellExperiment)
example(SingleCellExperiment, echo=FALSE)

bar <- function(x, i) reducedDim(x, i)
reducedDim(sce) # no problems
bar(sce)
## Error in reducedDim(x, i) : argument "i" is missing, with no default

The immediate fix in your example is to handle the missingness in foo:

foo <- function(object, i, j) {
    args <- list(x=object)
    if (!missing(i)) args$i <- i
    if (!missing(j)) args$j <- j
    do.call("[", args)
}

Not that it really matters because limma can't handle non-ordinary matrices anyway, so you might as well just coerce it to an ordinary matrix and be done with it.

Session information

R version 4.0.0 Patched (2020-05-01 r78341)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /home/luna/Software/R/R-4-0-branch-dev/lib/libRblas.so
LAPACK: /home/luna/Software/R/R-4-0-branch-dev/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] DelayedArray_0.15.6 IRanges_2.23.10     S4Vectors_0.27.12  
[4] BiocGenerics_0.35.4 matrixStats_0.56.0  Matrix_1.2-18      
[7] edgeR_3.31.4        limma_3.45.7       

loaded via a namespace (and not attached):
[1] compiler_4.0.0  tools_4.0.0     Rcpp_1.0.4.6    grid_4.0.0     
[5] locfit_1.5-9.4  lattice_0.20-41

[allisonvuong]

Hi,

Okay, thank you!

Best,
Allison

[hpages]

Thanks @LTLA for your help with this. Closing now.