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

5 messages · Felix Ernst, Vincent Carey, Martin Morgan +1 more

Original
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
Vincent Carey
# 
Confirmed with the following sessionInfo(), satisfying biocValid()==TRUE
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.ernst at ulb.ac.be> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
This email message may contain legally privileged and/or...{{dropped:2}}

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Hervé Pagès
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
      #
    

  


  

      
Hi Felix,

This should be addressed in S4Vectors 0.17.11. Thanks for the catch and
for the nice reproducible example.

Best,
H.

        
On 11/26/2017 04:09 AM, Felix Ernst wrote: