[Bioc-devel] "nearest" & related methods for GRangesList & friends?

Hello,

I recently found myself in want of a nearest method that handles
GRangesList objects. Is there any plan to add one?

I just want to define
"nearest" for elements of a GRangesList by the shortest distance between
any query range and any subject range. Obviously I can do this by
unlisting the GRangesList, calling nearest, and then post-processing to
figure out which element of the original GRangesList includes the
nearest range, but it would be nice to have a function that already does
this for me.

-Ryan

Hi Ryan,

On 05/22/2014 03:38 PM, Ryan C. Thompson wrote:

Hello,

I recently found myself in want of a nearest method that handles
GRangesList objects. Is there any plan to add one?

Not that I know of. I guess most of the times it's probably good enough
to call range() on both GRangesList objects before passing them to
nearest(). What's the use case for caring about "gaps" within each
GRangesList element?

I just want to define
"nearest" for elements of a GRangesList by the shortest distance between
any query range and any subject range. Obviously I can do this by
unlisting the GRangesList, calling nearest, and then post-processing to
figure out which element of the original GRangesList includes the
nearest range, but it would be nice to have a function that already does
this for me.

The easy one is a "nearest" method between a GRanges and a GRangesList.
Is it what you need? That would cover finding the nearest gene or
transcript for ChIPseq peaks when the exon structure actually matters
(seems like it would matter only for peaks that fall inside more than
1 transcript).

Or do you need a method that operates on 2 GRangesList objects? Can't
think of a use case for that one. Finding the nearest gene or transcript
for junction reads?

Thanks,
H.

-Ryan

Here is my use case (relevant lines highlighted):

https://gist.github.com/anonymous/0cd0c926fb21a8d62fcc#file-annotatepeaks-r-L49-L54


The idea is to annotate each peak with the Entrez ID of the nearest
transcription start site. Each Entrez ID can have multiple transcripts,
hence multiple TSS, so I basically want to call nearest with a GRanges
of peaks against a GRangesList of TSS (each TSS is a range with a width
of 1 containing the first base pair of a transcript). I don't personally
need a method that works for a GRangesList query.

-Ryan


On Fri 23 May 2014 11:13:24 AM PDT, Herv? Pag?s wrote:

Hi Ryan,

On 05/22/2014 03:38 PM, Ryan C. Thompson wrote:

Hello,

I recently found myself in want of a nearest method that handles
GRangesList objects. Is there any plan to add one?

Not that I know of. I guess most of the times it's probably good enough
to call range() on both GRangesList objects before passing them to
nearest(). What's the use case for caring about "gaps" within each
GRangesList element?

I just want to define
"nearest" for elements of a GRangesList by the shortest distance between
any query range and any subject range. Obviously I can do this by
unlisting the GRangesList, calling nearest, and then post-processing to
figure out which element of the original GRangesList includes the
nearest range, but it would be nice to have a function that already does
this for me.

The easy one is a "nearest" method between a GRanges and a GRangesList.
Is it what you need? That would cover finding the nearest gene or
transcript for ChIPseq peaks when the exon structure actually matters
(seems like it would matter only for peaks that fall inside more than
1 transcript).

Or do you need a method that operates on 2 GRangesList objects? Can't
think of a use case for that one. Finding the nearest gene or transcript
for junction reads?

Thanks,
H.

-Ryan