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]]
>>
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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@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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