[BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor

[Hervé Pagès]

Hi Malcolm,

On 08/13/2013 11:39 AM, Cook, Malcolm wrote:
> Hiya,
>
> I find that setting mcol of a GRanges to a DataFrame one of whose columns is an ordered factor does "the wrong thing".
>
> Not sure how to approach this other than report it for now.
>
> Best,
>
> Malcolm
>
>
>
> viz:
>
>> library(GenomicRanges)
>> example(GRangesList)
>> gr1
> GRanges with 1 range and 2 metadata columns:
>        seqnames    ranges strand |     score        GC
>           <Rle> <IRanges>  <Rle> | <integer> <numeric>
>    [1]     chr2    [3, 6]      + |         5      0.45
>    ---
>    seqlengths:
>     chr2
>       NA
>> mc1<-mcols(gr1)
>> mc1$f<-factor('x')
>> mcols(gr1)<-mc1
>> gr1
> GRanges with 1 range and 3 metadata columns:
>        seqnames    ranges strand |     score        GC        f
>           <Rle> <IRanges>  <Rle> | <integer> <numeric> <factor>
>    [1]     chr2    [3, 6]      + |         5      0.45        x
>    ---
>    seqlengths:
>     chr2
>       NA
>>   mc1$fo<-ordered('x')
>> mcols(gr1)<-mc1
>> gr1
> GRanges with 1 range and 4 metadata columns:
>        seqnames      ranges  strand   |       score          GC          f          fo
>         "<Rle>" "<IRanges>" "<Rle>" "|" "<integer>" "<numeric>" "<factor>" Character,2
>    [1]   "chr2"    "[3, 6]"     "+" "|"         "5"      "0.45"        "x"         "x"
>    ---
>    seqlengths:
>     chr2
>       NA

Thanks for the report. Note that this is a display bug only. Fixed in
IRanges 1.19.24:

   > gr1
   GRanges with 1 range and 4 metadata columns:
         seqnames    ranges strand |     score        GC        f        fo
            <Rle> <IRanges>  <Rle> | <integer> <numeric> <factor> <ordered>
     [1]     chr2    [3, 6]      + |         5      0.45        x         x
     ---
     seqlengths:
      chr2
        NA

Cheers,
H.


>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] GenomicRanges_1.12.4 IRanges_1.18.2       BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.1 tools_3.0.1
>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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