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

[Cook, Malcolm]

Great Herve,

Any chance of a back port to released version?

THx,

Malcolm

 >-----Original Message-----
 >From: Hervé Pagès [mailto:hpages at fhcrc.org]
 >Sent: Tuesday, August 13, 2013 2:33 PM
 >To: Cook, Malcolm
 >Cc: 'bioconductor at r-project.org'
 >Subject: Re: [BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor
 >
 >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
 >1100 Fairview Ave. N, M1-B514
 >P.O. Box 19024
 >Seattle, WA 98109-1024
 >
 >E-mail: hpages at fhcrc.org
 >Phone:  (206) 667-5791
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