[BioC] distanceToNearest for GRanges?

Valerie Obenchain vobencha at fhcrc.org
Mon Aug 20 22:48:13 CEST 2012

Hi Janet,

The precede() and follow() code has been completely rewritten in devel 
(as compared to release). Because nearest() and distanceToNearest() 
depend on these, updating in release will require the updating of all 
functions. This might be ok or this might be a problem as other packages 
(on which the code may depend)  have evolved in the devel branch. I'll 
look into this and post back when it is either done or I have more 


On 08/20/2012 11:57 AM, Janet Young wrote:
> Valerie Obenchain<vobencha at ...>  writes:
>> Hi Malcom,
>> For distanceToNearest() I started with the ranges method in IRanges.
>> Along the way I did find that distance,GenomicRanges,GenomicRanges was
>> not handling the situation of '*','-' and '*','+' strand pairs (simply
>> returning NA). Now those strand combinations are considered compatible
>> just as '-','-' and '+','+' are.
>> Let me know if you run into problems with the method or have other
>> suggestions.
>> Take care,
>> Valerie
> Hi there,
> I'm revisiting this older string.
> I'm still using the release versions of GenomicRanges and IRanges (I want to
>   spend a little time figuring out the useDevel stuff, but the pressure is on
>    to think about biology right now, and it seems it might be better for me
>    to stick to the release versions).
> That means distanceToNearest isn't available for GRanges in the version I'm
>   using, so I'm using a variant of Malcolm's function (thanks again!).
>   However, I realized that I'm running into the same issue with strands
>   that you brought up, Valerie, that "*"/"+" pairs were not recognized.
> For now I'll try to remember to "unstrand" my GRanges objects before using
> nearest, but I wondered if it's possible to update the nearest function in
> the release version of IRanges so that it deals with the strands better?
> thanks,
> Janet
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