[Bioc-devel] SummarizedExperiment: structure loss, when mixing matrix and data.frame data

[Felix Ernst]

Hi all,

I got different results constructing a SummarizedExperiment in 3.6 and 3.7. My question is, whether this is intentional or a bug.

library(GenomicRanges)
library(SummarizedExperiment)

nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colnames(counts) <- LETTERS[1:6]
rownames(counts) <- 1:nrows
counts2 <- counts-floor(counts)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                     IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                     strand=sample(c("+", "-"), 200, TRUE),
                     feature_id=sprintf("ID%03d", 1:200))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                     row.names=LETTERS[1:6])

se <- SummarizedExperiment(assays=list(counts=counts),
                           rowRanges=rowRanges,
                           colData=colData)

str(assays(se)$counts)
assays(se)$counts2 <- as.data.frame(counts2)
str(assays(se)$counts)

On a Windows 10 R3.4.2 Bioc 3.6 this produces:
num [1:200, 1:6] 8815 6314 1945 6185 5935 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:200] "1" "2" "3" "4" ...
  ..$ : chr [1:6] "A" "B" "C" "D" ...
 num [1:200, 1:6] 8815 6314 1945 6185 5935 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:200] "1" "2" "3" "4" ...
  ..$ : chr [1:6] "A" "B" "C" "D" ...

On Ubuntu 17.10 R-devel r73779 Bioc3.7  this produces
num [1:200, 1:6] 8636 7040 9275 4821 2475 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:200] "1" "2" "3" "4" ...
  ..$ : chr [1:6] "A" "B" "C" "D" ...
 num [1:1200] 8636 7040 9275 4821 2475 ...

Somehow the structure is lost. 

This happens, if I mix matrix and data.frame data, and doesn’t, if I use only matrices. The man page defines matrix-like objects, 
which a data.frame is (isn’t it?) and the behavior is different from Bioc3.6 to Bioc3.7. 

I can rule out that this is a Windows/Linux thing, because the Travis build error, which pointed to an difference in the first place,
didn‘t occur with bioc-release, just with bioc-devel.

Thanks for any advice and suggestions.

Felix

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