[BioC] GRangesList mcols names

[Valerie Obenchain]

The restriction has been removed in 1.13.53.

Val

On 10/09/2013 08:30 AM, Valerie Obenchain wrote:
> I'm ok with that.
>
> Val
>
> On 10/08/2013 06:16 PM, Michael Lawrence wrote:
>> I would say we should remove the restriction. It violates the
>> expectations of the user. One set of columns describes the individual
>> ranges, the other the GRanges as a whole.
>>
>>
>> On Tue, Oct 8, 2013 at 5:03 PM, Valerie Obenchain <vobencha at fhcrc.org
>> <mailto:vobencha at fhcrc.org>> wrote:
>>
>>     Hi Leonard,
>>
>>     This check was most likely put in place to avoid a name clash if the
>>     GRangesList was flattened and the mcols() on the GRangesList were
>>     rep'd out. I can't think of a function that currently does this but
>>     I might be overlooking something. At any rate, in v 1.13.52 I've
>>     moved the error up to the time of construction.
>>
>>      > mcols(grl)$x <- 1
>>     Error in .local(x, ..., value = value) :
>>
>>        'mcols(x)' cannot have columns named as metadata  columns of
>>     unlisted GRanges
>>
>>     Valerie
>>
>>
>>
>>     On 10/05/2013 10:14 PM, Leonard Goldstein wrote:
>>
>>         Dear list,
>>
>>         I noticed that GRangesList objects are not allowed to have outer
>>         elementMetadata columns with names identical to names of inner
>>         elementMetadata columns (see below)
>>
>>         Is this restriction necessary? And if yes, should identical
>>         names raise an
>>         exception at the time of construction rather than further down
>>         the line?
>>
>>         Best wishes,
>>
>>         Leonard
>>
>>
>>             gr <- GRanges("1", IRanges(1, 100), "x" = 1)
>>             grl <- split(gr, 1)
>>             mcols(grl)$x <- 1
>>             grl[1, ]
>>
>>         Error in validObject(.Object) :
>>             invalid class “GRangesList” object: 'mcols(x)' cannot have
>>         columns named
>>         as metadata  columns of unlisted GRanges
>>
>>
>>             sessionInfo()
>>
>>         R version 3.0.0 (2013-04-03)
>>         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] parallel  stats     graphics  grDevices utils     datasets
>>           methods
>>         [8] base
>>
>>         other attached packages:
>>         [1] GenomicRanges_1.13.50 XVector_0.1.4         IRanges_1.19.38
>>         [4] BiocGenerics_0.7.5
>>
>>         loaded via a namespace (and not attached):
>>         [1] stats4_3.0.0
>>
>>
>>
>>                  [[alternative HTML version deleted]]
>>
>>
>>
>>         _________________________________________________
>>         Bioconductor mailing list
>>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>         https://stat.ethz.ch/mailman/__listinfo/bioconductor
>>         <https://stat.ethz.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>
>>
>>
>>     _________________________________________________
>>     Bioconductor mailing list
>>     Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>     https://stat.ethz.ch/mailman/__listinfo/bioconductor
>>     <https://stat.ethz.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>
>>
>>
>
> _______________________________________________
> 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