[Bioc-devel] GenomicRanges: Concatenation of GRanges with matrices in mcols

[Hervé Pagès]

Hi Julian,

At the root of the problem is what rbind() does on DataFrames containing
matrices:

   m <- matrix(1:4, nrow=2)
   df <- DataFrame(m=I(m))
   df2 <- rbind(df, df)

Then:

   > df2
   DataFrame with 8 rows and 1 column
            m
     <matrix>
   1      1 3
   2      2 4
   3      1 3
   4      2 4

   > nrow(df2)
   [1] 8

Too many rows!

   > str(df2)
   Formal class 'DataFrame' [package "IRanges"] with 6 slots
     ..@ rownames       : NULL
     ..@ nrows          : int 12
     ..@ listData       :List of 1
     .. ..$ m: int [1:6, 1:2] 1 2 3 1 2 3 4 5 6 4 ...
     ..@ elementType    : chr "ANY"
     ..@ elementMetadata: NULL
     ..@ metadata       : list()

   > validObject(df2)
   [1] TRUE

I'll leave this to Michael.

Thanks,
H.


On 05/20/2014 01:22 AM, Julian Gehring wrote:
> Hi,
>
> If I want to bind two GRanges object with a matrix in the meta columns,
> the concatenation of the two fails in bioc-stable (GenomicRanges 1.16.3)
> and bioc-devel (GenomicRanges 1.17.13) with:
>
> '''
> Error in validObject(.Object) :
>    invalid class “GRanges” object: number of rows in DataTable
> 'mcols(x)' must match length of 'x'
> '''
>
> If multiple columns are used, the class of of the first column seem to
> determine the behavior:
>
> #+BEGIN_SRC R
>    library(GenomicRanges)
>
>    ## sample data, two identical GRanges
>    gr1 = gr2 = GRanges(1, IRanges(1:2, width = 1))
>    m = matrix(1:4, 2)
>
>    ## the vector alone works
>    mcols(gr1) = mcols(gr2) = DataFrame(x = 1)
>    c(gr1, gr2) ## works
>
>    ## vector first, matrix second works
>    mcols(gr1) = mcols(gr2) = DataFrame(x = 1, m = I(m))
>    c(gr1, gr2) ## works
>
>    ## the matrix alone fails
>    mcols(gr1) = mcols(gr2) = DataFrame(m = I(m))
>    c(gr1, gr2) ## fails
>
>    ## matrix first, vector second fails
>    mcols(gr1) = mcols(gr2) = DataFrame(m = I(m), x = 1)
>    c(gr1, gr2) ## fails
> #+END_SRC
>
> Best wishes
> Julian
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Program in Computational Biology
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