[BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?

[Steve Lianoglou]

On Thu, Oct 14, 2010 at 5:55 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
<snip>
> As an update, Patrick has improved performance 10x-ish in IRanges
> 1.7.40, still some more to go...
>
>> replicate(5, system.time(lapply(xcripts, length)))
>           [,1]  [,2]  [,3]  [,4]  [,5]
> user.self  0.31 0.317 0.318 0.313 0.328
> sys.self   0.00 0.002 0.000 0.002 0.000
> elapsed    0.31 0.325 0.319 0.317 0.329
> user.child 0.00 0.000 0.000 0.000 0.000
> sys.child  0.00 0.000 0.000 0.000 0.000
>
>> irl <- IRangesList(lapply(xcripts, ranges))
>
>> replicate(5, system.time(lapply(irl, length)))
>            [,1]  [,2]  [,3]  [,4]  [,5]
> user.self  0.032 0.031 0.032 0.031 0.030
> sys.self   0.000 0.000 0.000 0.001 0.001
> elapsed    0.032 0.031 0.032 0.032 0.031
> user.child 0.000 0.000 0.000 0.000 0.000
> sys.child  0.000 0.000 0.000 0.000 0.000

Awesome!

Thanks for dumping some brain power into this.

Out of curiosity: I have several lists of serialized GRanges objects
which I had to regenerate with the introduction of isCircular (or
whatever it was) because of binary incompatibility with old/new
versions of GRanges.

Do these updates break any binary compatibility or anything? I'm not
complaining, I just want to make sure I avoid updating until I can get
"out of the woods" and find time to regenerate these things ;-).

Thanks,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact