[Bioc-devel] GenomicFiles: some random issues

[Michael Lawrence]

Added a new vignette to GenomicRanges that explains this stuff.

On Mon, Sep 29, 2014 at 6:54 PM, Michael Lawrence <michafla at gene.com> wrote:

> I admit negligence in not document this. But if you look at VRanges, you
> can see how we set a method for "extraColumnSlotNames" returns a character
> vector of slot names to tell GenomicRanges which slots should be treated as
> columns (there is also an example in the previous email). These are then
> handled automatically in subsetting, showing, validation, etc. This has
> also been used in the exonfindR package (just submitted to Bioc). I'll put
> documenting that feature on the TODO list.
>
> Michael
>
> On Mon, Sep 29, 2014 at 5:08 PM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> Based on Chuck's email I realize I did not understand Michael's answer at
>> all.
>>
>> On Mon, Sep 29, 2014 at 7:44 PM, Charles Berry <ccberry at ucsd.edu> wrote:
>>
>> > Michael Lawrence <lawrence.michael <at> gene.com> writes:
>> >
>> > >
>> > > This comes down to an inheritance vs. composition decision, but I hope
>> > > everyone is aware of the extraColumnSlots mechanism in GRanges that
>> makes
>> > > it easy to add additional "column-shaped" slots to a subclass of
>> GRanges.
>> >
>> > Where is it documented, please?
>> >
>> > Chuck
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
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>
>

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