[Bioc-devel] could bsseq::data.frame2GRanges be added to GenomicRanges

[Steve Lianoglou]

Hi,

+1 from me, too ... I've also had a similar conversion function
(data.[frame|table] <--> GRanges) in my toolbelt which I found quite
useful over the years.

-steve

On Sun, Oct 6, 2013 at 5:00 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> This is a convenience function, which provably has saved tons of time for
> me and others.  I get lots of data from various excel/cvs files lying
> around various places, and these files _always_ have a clear path to a
> GRanges.  Perhaps you never have to deal with this kind of data, but we are
> a few experienced users who find it extremely handy and would like it to be
> in a more centralized place.
>
>
>
>
>
> On Sun, Oct 6, 2013 at 4:26 PM, Michael Lawrence
> <lawrence.michael at gene.com>wrote:
>
>> I'm still unconvinced that there is an obvious, general path from
>> data.frame -> GRanges. It's usually easy enough to just call GRanges(),
>> often of the pattern with(df, GRanges(...)). Moreover, it's unusual for me
>> to encounter genomic data in data.frames.
>>
>>
>>
>>
>> On Sun, Oct 6, 2013 at 8:37 AM, Kasper Daniel Hansen <
>> kasperdanielhansen at gmail.com> wrote:
>>
>>> Also, it goes without saying that I am happy to provide a patch for
>>> GenomicRanges, and check that it passes R CMD check, to minimize the work
>>> of the maintainer.
>>>
>>> Kasper
>>>
>>>
>>> On Sun, Oct 6, 2013 at 9:28 AM, Kasper Daniel Hansen <
>>> kasperdanielhansen at gmail.com> wrote:
>>>
>>> > bsseq::data.frame2GRanges does the obvious step of converting a
>>> data.frame
>>> > to GRanges.  It has a couple of bells and whistles where strand can be
>>> > ignored and additional columns (apart from genomic location) may be
>>> ignore
>>> > in the output object.
>>> >
>>> > I (and now quite a few other people) use this function almost every day.
>>> >  I have seen other implementations in other packages, suggesting this is
>>> > not just something I (we) use.
>>> >
>>> > I suggests adding this function to GenomicRanges.  I am happy to support
>>> > it going forward.
>>> >
>>> > Using this function we could also add an as(x, "GRanges") method for
>>> > x=data.frame, but I still suggest keeping the basic function for the
>>> > extended functionality it provides.
>>> >
>>> > Best,
>>> > Kasper
>>> >
>>>
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>>>
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>>
>>
>
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>
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-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech