[Bioc-devel] mcols<-() behaviour inheriting from Vector vs GRanges

[Hervé Pagès]

This is fixed in S4Vectors release (0.8.6) and devel (0.9.16).

Cheers,
H.

On 01/04/2016 11:52 AM, Hervé Pagès wrote:
> Hi Malcolm,
>
> Thanks for reporting this. Will fix.
>
> H.
>
> On 01/04/2016 10:53 AM, Malcolm Perry wrote:
>> Hello,
>>
>> A recent question on the support site (
>> https://support.bioconductor.org/p/76430/#76460) shows that the mcols
>> assignment in GRanges (and perhaps others) is subtly different from
>> classes
>> that purely inherit from Vector (such as GenomicInteractions in the
>> example), as the GRanges method will implicitly convert a data.frame
>> object
>> to a "DataFrame".
>>
>> Is it possible for Vector to have the same behaviour? From the users'
>> perspective it looks like a bug in the downstream package, and I guess
>> many
>> people will not spot the obvious fix.
>>
>> Thanks,
>>
>> Malcolm
>>
>> PS Here is a self-contained example just using the core packages and no
>> external data:
>>
>> library(S4Vectors)
>>
>> setClass("CharacterVector",
>>      representation(char_data = "character"),
>>      contains="Vector"
>> )
>>
>> setMethod(length, "CharacterVector", function(x) length(x at char_data))
>>
>> char = new("CharacterVector", char_data=c("one", "two", "three"))
>>
>> mcols(char) = data.frame(number=1:3) # will fail
>>
>> mcols(char) = DataFrame(number=1:3) # fine
>>
>> library(GenomicRanges)
>>
>> gr = GRanges("chr", IRanges(1, 5))
>>
>> mcols(gr) = data.frame(name="range1")
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

-- 
Hervé Pagès

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