[BioC] GRanges() and naming of metadata columns has changed

[Hervé Pagès]

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]]
>
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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

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