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

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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