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

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]]

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

Cheers,
H.


On 01/04/2016 11:52 AM, Herv? Pag?s 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]]

--
Herv? Pag?s

Program in Computational Biology
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