BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor
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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 3 months ago
United States
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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@herve-pages-1542
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Seattle, WA, United States
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 >> > > _______________________________________________ > Bioconductor mailing list > 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
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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 >>> >> >> _______________________________________________ >> Bioconductor mailing list >> 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
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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 > >>> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> 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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