Unable to use correctExperiments with 'subset.row=' defined

[ycl6]

Hi,

There is a problem using correctExperiments with subset.row= flag to subset assays to the defined genes. I am using the function on a list of SingleCellExperiments.

batchelor/R/correctExperiments.R

Lines 100 to 102 in ea09e98

	if (!is.null(subset.row) && !correct.all) {
	raw.ass <- lapply(raw.ass, "[", i=subset.row, , drop=FALSE)
	}

Error in eval(subscript, envir = eframe, enclos = eframe): '...' used in an incorrect context
Traceback:

1. lapply(raw.ass, "[", i = subset.row, , drop = FALSE)
2. lapply(raw.ass, "[", i = subset.row, , drop = FALSE)
3. FUN(X[[i]], ...)
4. FUN(X[[i]], ...)
5. extract_Nindex_from_syscall(sys.call(), parent.frame())
6. lapply(seq_len(length(call) - 2L), function(i) {
 .     subscript <- call[[2L + i]]
 .     if (missing(subscript)) 
 .         return(NULL)
 .     subscript <- eval(subscript, envir = eframe, enclos = eframe)
 .     if (is.null(subscript)) 
 .         return(integer(0))
 .     subscript
 . })
7. lapply(seq_len(length(call) - 2L), function(i) {
 .     subscript <- call[[2L + i]]
 .     if (missing(subscript)) 
 .         return(NULL)
 .     subscript <- eval(subscript, envir = eframe, enclos = eframe)
 .     if (is.null(subscript)) 
 .         return(integer(0))
 .     subscript
 . })
8. FUN(X[[i]], ...)
9. eval(subscript, envir = eframe, enclos = eframe)
10. eval(subscript, envir = eframe, enclos = eframe)
11. eval(subscript, envir = eframe, enclos = eframe)

I propose changed it as below and that should work.

        if (!is.null(subset.row) && !correct.all) {
            raw.ass <- lapply(raw.ass, function(x) x[subset.row,,drop=FALSE])
        }

R version 4.1.0 (2021-05-18)
batchelor_1.8.0

[LTLA]

This seems like a problem with DelayedArray rather than batchelor, see Bioconductor/DelayedArray#97.

[ycl6]

Thanks @LTLA , hope that either DelayedArray or batchelor is fixed for the function to work properly.

[MerRome]

Hello,

I am still observing the same problem with batchelor_1.12.0 and DelayedArray version 0.22.0, do you have any suggestions or workarounds?

Thanks for your time!
Merrit

[LTLA]

Gave up waiting for DelayedArray to fix it so I just patched it on correctExperiments's end.