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

[Hervé Pagès]

On 05/20/2014 12:49 PM, Hervé Pagès wrote:
> 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()

Sorry, I mixed up outputs from different sessions. Correct str() output:

   > str(df2)
   Formal class 'DataFrame' [package "IRanges"] with 6 slots
     ..@ rownames       : NULL
     ..@ nrows          : int 8
     ..@ listData       :List of 1
     .. ..$ m: int [1:4, 1:2] 1 2 1 2 3 4 3 4
     ..@ elementType    : chr "ANY"
     ..@ elementMetadata: NULL
     ..@ metadata       : list()

H.

>
>    > 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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