[Bioc-devel] Unexpected behaviour with Assays and Vector classes

[Aaron Lun]

Hello all,

I've encountered some unexpected behaviour with some of the base classes 
while developing stuff for genomic interactions. The first issue lies 
with the subset replacement in the Vector class. Let's say I make a 
derived class "foo" inheriting from Vector, as below:

 > require(S4Vectors)
 > setClass("foo", contains="Vector", slots=c(blah="integer"))
 > setMethod("parallelSlotNames", "foo", function(x) {
 >     c("blah", callNextMethod())
 > })
[1] "parallelSlotNames"
 > setMethod("c", "foo", function(x, ..., recursive=TRUE) {
 >    new.blah <- do.call(c, lapply(list(x, ...), FUN=slot, name="blah"))
 >    new.mcols <- do.call(rbind, lapply(list(x, ...), FUN=mcols))
 >    new("foo", blah=new.blah, metadata=metadata(x),
 >        elementMetadata=new.mcols)
 > })
[1] "c"

Construction gives what you'd expect:

 > a <- new("foo", blah=1:5, elementMetadata=DataFrame(stuff=1:5))
 > a at blah
[1] 1 2 3 4 5
 > mcols(a)$stuff
[1] 1 2 3 4 5

However, if I try to do subset replacement, I get this:

 > a[1] <- a[2]
 > a at blah
[1] 2 2 3 4 5
 > mcols(a)$stuff
[1] 1 2 3 4 5

So, "blah" is replaced properly, but "elementMetadata" is not. This is 
attributable to a line in "replaceROWS" which preserves the mcols of the 
original object during replacement (also for "names"). Should this line 
be removed to give expected behaviour for the elementMetadata?

The other issue is that r/cbind'ing doesn't seem to work properly for 
unnamed multi-matrix Assays objects. Consider:

 > require(SummarizedExperiment)
 > whee <- Assays(list(x1=matrix(1, 3, 4), x2=matrix(2, 3, 4)))
 > whee2 <- Assays(list(x1=matrix(3, 3, 4), x2=matrix(4, 3, 4)))
 > rbind(whee, whee2)
Reference class object of class "ShallowSimpleListAssays"
Field "data":
List of length 2
names(2): x1 x2
 >
 > names(whee) <- names(whee2) <- NULL
 > rbind(whee, whee2)
Reference class object of class "ShallowSimpleListAssays"
Field "data":
List of length 1

So, unnaming and rbind'ing results in the loss of a matrix. This is the 
same issue I reported for unnamed multi-matrix assays when rbinding 
multiple SummarizedExperiment objects; I recall that being resolved by 
r/cbind'ing based on position. Should this be done here as well? If not, 
perhaps we should force people to name their assays.

Cheers,

Aaron

 > sessionInfo()
R Under development (unstable) (2015-10-30 r69588)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)

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] SummarizedExperiment_1.1.2 Biobase_2.31.0
[3] GenomicRanges_1.23.3       GenomeInfoDb_1.7.3
[5] IRanges_2.5.5              S4Vectors_0.9.8
[7] BiocGenerics_0.17.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.17.0 XVector_0.11.0