On Mon, Nov 30, 2009 at 11:10 AM, Charles C. Berry <cberry@tajo.ucsd.edu>wrote:

>
>
> The semantics of the IRanges package and especially the RangedData class
> are very apprpriate for some of the applications I deal with.
>
> Unfortunately, coverage() is too slow to be useful to me.
>
> I wonder if the Biocore Team would consider retooling it to make it
> faster? Below I provide a link to a revised coverage.c that might suffice.
>
> The kind of case I need to handle has width values in 10kbase to 10Mbase
> range. As a toy example, being able to run stuff like
>
>      tmp <- coverage( IRanges( start=seq(1,by=1000,length=10000),
>                        width=1e7 ) )
>
> quickly is needed.
>
> A revised version of coverage.c is available at
>
> http://cabig2.ucsd.edu:8080/Plone/Members/ccberry/software/coverage.c/view
>
> It will handle the case above almost instantly (while the existing version
> needs about 8 minutes on my machine) and seems about equal to the
> existing version for cases with width=30.  In the cases I've looked at
> gc() reports the same memory usage.
>
> ---
>
> Also, I wonder if the Biocore Team would entertain allowing the 'weight'
> argument of coverage to be of type double? This would help in cases in
> which downweighting of counts of some genomic features is desired.
>
>
In many use cases, it's probably sufficient to simply round floating point
numbers to integers after multiplying by a power of 10. That only goes so
far though, so supporting double-precision seems reasonable. The type of the
output will simply depend on the type of the weights.



> Thanks,
>
> Chuck
>
> --
> Charles C. Berry                            (858) 534-2098
>                                            Dept of Family/Preventive
> Medicine
> E mailto:cberry@tajo.ucsd.edu               UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>
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