[BioC] Turning a GRanges Metadata Column into Rle List

[Tim Triche, Jr.]

Something like 

coverage(foo, bar, ..., NA.value=-1)

?

--t

On Jan 7, 2013, at 8:59 AM, Michael Lawrence <lawrence.michael at gene.com> wrote:

> One hack would be to add 1 to all of the scores, replace the zeros in the
> coverage() result with NAs and subtract 1. I've hit something like this a
> couple times in the past. The coverage method for GRanges could gain a
> default value argument.
> 
> Michael
> 
> 
> 
> On Sun, Jan 6, 2013 at 11:00 PM, Dario Strbenac <D.Strbenac at garvan.org.au>wrote:
> 
>>>  coverage(g, weight=values(g)$scores)
>> 
>> That is close to what I was after, although the ranges which aren't
>> present in the GRanges object effectively have missing scores and need to
>> be NA because 0 is a valid score for the ranges which are present. So, if I
>> had a view defined that only partially overlapped with a range in the
>> example, I would want any summary to give NA, rather than taking 0 into the
>> calculation.
>> 
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