[BioC] GRangesList mcols names
Valerie Obenchain
vobencha at fhcrc.org
Wed Oct 9 20:35:28 CEST 2013
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]]
>>
>>
>>
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