[BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor
Hervé Pagès
hpages at fhcrc.org
Tue Aug 13 22:54:01 CEST 2013
On 08/13/2013 01:29 PM, Cook, Malcolm wrote:
> Great Herve,
>
> Any chance of a back port to released version?
Sure. Back ported to IRanges 1.18.3.
H.
>
> 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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> >> Bioconductor at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >--
> >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
> >Fax: (206) 667-1319
>
--
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
Fax: (206) 667-1319
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