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

[Cook, Malcolm]

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
> 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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