GRanges() and naming of metadata columns has changed

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

I think this commit: ---------------------------------------------------------------------- -- r73720 | hpages@fhcrc.org | 2013-02-24 23:17:38 -0800 (Sun, 24 Feb 2013) | 3 lines Tweak to GRanges() constructor so the names of the supplied metadata cols don't run in conflict with some obscure internal argument names. ---------------------------------------------------------------------- -- Means that we can no longer do this: mycol <- 1 GRanges("chr1", IRanges(1, 10), "+", mycol) And get a GRanges with a metadata column named "mycol" like we get with DataFrame and data.frame. This is a pretty big change in behavior that is breaking code. In other words, we now get this: GRanges with 1 range and 1 metadata column: seqnames ranges strand | *1* <rle> <iranges> <rle> | <numeric> [1] chr1 [1, 10] + | 1 --- seqlengths: chr1 NA While I'm pretty sure we used to get: GRanges with 1 range and 1 metadata column: seqnames ranges strand | *mycol* <rle> <iranges> <rle> | <numeric> [1] chr1 [1, 10] + | 1 --- seqlengths: chr1 NA Michael R Under development (unstable) (2013-03-27 r62427) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] isoseq_0.0.8 Rsamtools_1.11.27 [3] Biostrings_2.27.13 org.Hs.eg.db_2.9.0 [5] RSQLite_0.11.2 DBI_0.2-5 [7] TxDb.Hsapiens.BioMart.igis_2.1.2 GenomicFeatures_1.11.16 [9] AnnotationDbi_1.21.16 Biobase_2.19.3 [11] GenomicRanges_1.11.42 IRanges_1.17.41 [13] BiocGenerics_0.5.6 CGPtools_2.0.54 loaded via a namespace (and not attached): [1] annotate_1.37.4 biomaRt_2.15.1 biovizBase_1.7.8 [4] bitops_1.0-5 BSgenome_1.27.1 cluster_1.14.4 [7] colorspace_1.2-1 DESeq_1.11.6 dichromat_2.0-0 [10] digest_0.6.3 genefilter_1.41.4 geneplotter_1.37.0 [13] ggbio_1.7.14 ggplot2_0.9.3.1 grid_3.1.0 [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.10-1 [19] labeling_0.1 lattice_0.20-15 MASS_7.3-26 [22] Matrix_1.0-12 munsell_0.4 plyr_1.8 [25] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 [28] reshape2_1.2.2 rjson_0.2.12 rtracklayer_1.19.11 [31] scales_0.2.3 splines_3.1.0 stats4_3.1.0 [34] stringr_0.6.2 survival_2.37-4 VariantAnnotation_1.5.45 [37] XML_3.96-0.2 xtable_1.7-1 zlibbioc_1.5.0 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.1 years ago by Hervé Pagès 16k • written 11.1 years ago by Michael Lawrence ★ 11k

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Hervé Pagès 16k

@herve-pages-1542

Last seen 6 hours ago

Seattle, WA, United States

Hi Michael, On 04/05/2013 10:32 AM, Michael Lawrence wrote: > I think this commit: > > -------------------------------------------------------------------- ---- > r73720 | hpages at fhcrc.org | 2013-02-24 23:17:38 -0800 (Sun, 24 Feb 2013) | > 3 lines > > Tweak to GRanges() constructor so the names of the supplied metadata cols > don't > run in conflict with some obscure internal argument names. > > -------------------------------------------------------------------- ---- > > Means that we can no longer do this: > > mycol <- 1 > GRanges("chr1", IRanges(1, 10), "+", mycol) > > And get a GRanges with a metadata column named "mycol" like we get with > DataFrame and data.frame. This is a pretty big change in behavior that is > breaking code. > > In other words, we now get this: > GRanges with 1 range and 1 metadata column: > seqnames ranges strand | *1* > <rle> <iranges> <rle> | <numeric> > [1] chr1 [1, 10] + | 1 > --- > seqlengths: > chr1 > NA > > While I'm pretty sure we used to get: > GRanges with 1 range and 1 metadata column: > seqnames ranges strand | *mycol* > <rle> <iranges> <rle> | <numeric> > [1] chr1 [1, 10] + | 1 > --- > seqlengths: > chr1 > NA Ooops, seems like that change introduced a regression. The change was made in response to this bug: > GRanges("chr1", IRanges(1:3, 10), "+", c=mycol) Error in .getClassFromCache(Class, where) : Class should be either a character-string name or a class definition reported on Bioc-devel back in February: https://stat.ethz.ch/pipermail/bioc-devel/2013-February/004096.html Just committed my second attempt at fixing this. Shouldn't break passing of unnamed metadata cols anymore. Thanks for the catch, H. > > Michael > > R Under development (unstable) (2013-03-27 r62427) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools parallel stats graphics grDevices utils datasets > > [8] methods base > > other attached packages: > [1] isoseq_0.0.8 Rsamtools_1.11.27 > [3] Biostrings_2.27.13 org.Hs.eg.db_2.9.0 > [5] RSQLite_0.11.2 DBI_0.2-5 > [7] TxDb.Hsapiens.BioMart.igis_2.1.2 GenomicFeatures_1.11.16 > [9] AnnotationDbi_1.21.16 Biobase_2.19.3 > [11] GenomicRanges_1.11.42 IRanges_1.17.41 > [13] BiocGenerics_0.5.6 CGPtools_2.0.54 > > loaded via a namespace (and not attached): > [1] annotate_1.37.4 biomaRt_2.15.1 > biovizBase_1.7.8 > [4] bitops_1.0-5 BSgenome_1.27.1 > cluster_1.14.4 > [7] colorspace_1.2-1 DESeq_1.11.6 > dichromat_2.0-0 > [10] digest_0.6.3 genefilter_1.41.4 > geneplotter_1.37.0 > [13] ggbio_1.7.14 ggplot2_0.9.3.1 > grid_3.1.0 > [16] gridExtra_0.9.1 gtable_0.1.2 > Hmisc_3.10-1 > [19] labeling_0.1 lattice_0.20-15 > MASS_7.3-26 > [22] Matrix_1.0-12 munsell_0.4 > plyr_1.8 > [25] proto_0.3-10 RColorBrewer_1.0-5 > RCurl_1.95-4.1 > [28] reshape2_1.2.2 rjson_0.2.12 > rtracklayer_1.19.11 > [31] scales_0.2.3 splines_3.1.0 > stats4_3.1.0 > [34] stringr_0.6.2 survival_2.37-4 > VariantAnnotation_1.5.45 > [37] XML_3.96-0.2 xtable_1.7-1 > zlibbioc_1.5.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

ADD COMMENT • link 11.1 years ago Hervé Pagès 16k

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Thanks a lot for your quick fix, Herve! Michael On Fri, Apr 5, 2013 at 3:44 PM, Hervé Pagès <hpages@fhcrc.org> wrote: > Hi Michael, > > > On 04/05/2013 10:32 AM, Michael Lawrence wrote: > >> I think this commit: >> >> ------------------------------**------------------------------** >> ------------ >> r73720 | hpages@fhcrc.org | 2013-02-24 23:17:38 -0800 (Sun, 24 Feb 2013) >> | >> 3 lines >> >> Tweak to GRanges() constructor so the names of the supplied metadata cols >> don't >> run in conflict with some obscure internal argument names. >> >> ------------------------------**------------------------------** >> ------------ >> >> Means that we can no longer do this: >> >> mycol <- 1 >> GRanges("chr1", IRanges(1, 10), "+", mycol) >> >> And get a GRanges with a metadata column named "mycol" like we get with >> DataFrame and data.frame. This is a pretty big change in behavior that is >> breaking code. >> >> In other words, we now get this: >> GRanges with 1 range and 1 metadata column: >> seqnames ranges strand | *1* >> >> <rle> <iranges> <rle> | <numeric> >> [1] chr1 [1, 10] + | 1 >> --- >> seqlengths: >> chr1 >> NA >> >> While I'm pretty sure we used to get: >> GRanges with 1 range and 1 metadata column: >> seqnames ranges strand | *mycol* >> >> <rle> <iranges> <rle> | <numeric> >> [1] chr1 [1, 10] + | 1 >> --- >> seqlengths: >> chr1 >> NA >> > > Ooops, seems like that change introduced a regression. The change was > made in response to this bug: > > > GRanges("chr1", IRanges(1:3, 10), "+", c=mycol) > Error in .getClassFromCache(Class, where) : > Class should be either a character-string name or a class definition > > reported on Bioc-devel back in February: > > https://stat.ethz.ch/**pipermail/bioc- devel/2013-**February/004096.html<https: stat.ethz.ch="" pipermail="" bioc-="" devel="" 2013-february="" 004096.html=""> > > Just committed my second attempt at fixing this. Shouldn't break > passing of unnamed metadata cols anymore. > > Thanks for the catch, > H. > > > >> Michael >> >> R Under development (unstable) (2013-03-27 r62427) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tools parallel stats graphics grDevices utils datasets >> >> [8] methods base >> >> other attached packages: >> [1] isoseq_0.0.8 Rsamtools_1.11.27 >> [3] Biostrings_2.27.13 org.Hs.eg.db_2.9.0 >> [5] RSQLite_0.11.2 DBI_0.2-5 >> [7] TxDb.Hsapiens.BioMart.igis_2.**1.2 GenomicFeatures_1.11.16 >> [9] AnnotationDbi_1.21.16 Biobase_2.19.3 >> [11] GenomicRanges_1.11.42 IRanges_1.17.41 >> [13] BiocGenerics_0.5.6 CGPtools_2.0.54 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.37.4 biomaRt_2.15.1 >> biovizBase_1.7.8 >> [4] bitops_1.0-5 BSgenome_1.27.1 >> cluster_1.14.4 >> [7] colorspace_1.2-1 DESeq_1.11.6 >> dichromat_2.0-0 >> [10] digest_0.6.3 genefilter_1.41.4 >> geneplotter_1.37.0 >> [13] ggbio_1.7.14 ggplot2_0.9.3.1 >> grid_3.1.0 >> [16] gridExtra_0.9.1 gtable_0.1.2 >> Hmisc_3.10-1 >> [19] labeling_0.1 lattice_0.20-15 >> MASS_7.3-26 >> [22] Matrix_1.0-12 munsell_0.4 >> plyr_1.8 >> [25] proto_0.3-10 RColorBrewer_1.0-5 >> RCurl_1.95-4.1 >> [28] reshape2_1.2.2 rjson_0.2.12 >> rtracklayer_1.19.11 >> [31] scales_0.2.3 splines_3.1.0 >> stats4_3.1.0 >> [34] stringr_0.6.2 survival_2.37-4 >> VariantAnnotation_1.5.45 >> [37] XML_3.96-0.2 xtable_1.7-1 >> zlibbioc_1.5.0 >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]

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