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

[Martin Morgan]

On 10/14/2010 04:04 PM, Steve Lianoglou wrote:
> 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 ;-).

No, the speed-up did not involve changes in class structure.

Have you tried updateObject on your objects?

Martin

> 
> Thanks,
> -steve
> 


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