Hi,
Looks like at an even lower level, S4Vectors:::listElementType()
is at the origin of the problem:
> S4Vectors:::listElementType(list(matrix(), data.frame()))
[1] "vector"
Should return "ANY" here.
Will try to fix.
H.
On 11/26/2017 07:03 AM, Martin Morgan wrote:
It would seem to be a bug in endoapply
lst <- SimpleList(
m = matrix(0, 2, 2, dimnames=list(letters[1:2], LETTERS[1:2])),
df = data.frame(A=1:2, B=1:2, row.names=letters[1:2])
)
dimnames(lst[[1]]) # list(c("a", "b"), c("A", "B"))
dimnames(endoapply(lst, identity)[[1]]) # NULL
specifically S4Vectors:::coerceToSimpleList
lst <- list(
m = matrix(0, 2, 2, dimnames=list(letters[1:2], LETTERS[1:2])),
df = data.frame(A=1:2, B=1:2, row.names=letters[1:2])
)
S4Vectors:::coerceToSimpleList(lst)
Martin
On 11/26/2017 07:56 AM, Vincent Carey wrote:
Confirmed with the following sessionInfo(), satisfying biocValid()==TRUE
sessionInfo()
R Under development (unstable) (2017-11-22 r73776)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.1
Matrix products: default
BLAS: /home/stvjc/R-35-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-35-dist/lib/R/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] SummarizedExperiment_1.9.2 DelayedArray_0.5.5
[3] matrixStats_0.52.2 Biobase_2.39.0
[5] GenomicRanges_1.31.1 GenomeInfoDb_1.15.1
[7] IRanges_2.13.4 S4Vectors_0.17.10
[9] BiocGenerics_0.25.0
loaded via a namespace (and not attached):
[1] lattice_0.20-35 bitops_1.0-6 grid_3.5.0
[4] zlibbioc_1.25.0 XVector_0.19.1 Matrix_1.2-12
[7] tools_3.5.0 RCurl_1.95-4.8 compiler_3.5.0
[10] GenomeInfoDbData_0.99.2
On Sun, Nov 26, 2017 at 7:09 AM, Felix Ernst <felix.er...@ulb.ac.be>
wrote:
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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