[Bioc-sig-seq] Cached GenomicRanges or RangedData Objects?

[Charles C. Berry]

On Mon, 11 Oct 2010, Michael Lawrence wrote:

> I have a pass-by-reference GRanges that I have been playing around with for
> interactive graphics. I'll stick the package into svn soon.
>

Thanks. We'll look forward to trying that out.

> Also I'd point out that rtracklayer has bigWig support, which lets you
> access smaller portions of your data fairly efficiently.
>

Will check this out, too.

> Michael
>
> On Mon, Oct 11, 2010 at 10:51 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> When you are saying you're bumping up against the limits of RAM, how
>> much do you have?  It might be nice to have a GRanges that has
>> pass-by-reference semantics, but in general I find my GRanges to be
>> smaller (at most a couple of GB).  My "problems" are with the
>> associated data.
>>

Likewise. The GRanges aren't prohibitive, but every bit helps. Also, if we 
want to hand this software to others, it would be nice to not have to 
require others to mimic our hardware.

Chuck


>> Kasper
>>
>> On Mon, Oct 11, 2010 at 11:59 AM, Charles C. Berry <cberry at tajo.ucsd.edu>
>> wrote:
>>> On Mon, 11 Oct 2010, Steve Lianoglou wrote:
>>>
>>>> Hi Chuck,
>>>>
>>>> On Mon, Oct 11, 2010 at 11:24 AM, Charles C. Berry <
>> cberry at tajo.ucsd.edu>
>>>> wrote:
>>>>>
>>>>> We are liking the idioms that go with GenomicRanges and RangedData
>>>>> Objects
>>>>> (follow, precede, findOverlaps, etc), but we are bumping up against
>>>>> memory
>>>>> demands of loading very large objects.
>>>>>
>>>>> Is there now or will there soon be a cached version of these that will
>>>>> lessen our memory requirements?
>>>>>
>>>>> If not, is there a cookbook as to how to create and save cached
>> versions
>>>>> of
>>>>> these objects.
>>>>>
>>>>> Or maybe a place to look in the bioConductor codebase to get some ideas
>>>>> of
>>>>> how to go about constructing cached versions of these classes?
>>>>
>>>> I'm not sure what you mean by caching -- do you want them serialized
>>>> to disk and you read off parts when you need them, or?
>>>
>>> That's basically the idea. I looked at how BSGenome handles FASTA, and it
>>> allows you to read in one chromosome, make apparent copies that do not
>>> physically copy the object unless it is modified, and then clean up
>>> afterwards without much of the work under the hood.
>>>
>>>
>>>>
>>>> Also -- I typically split my data and processing to work on a
>>>> chromosome by chromosome basis -- even though the GenomicRanges
>>>> infrastructure allows you to keep ranges spanning multiple chromosomes
>>>> in one object. Although it's a bit more book keeping code on my part,
>>>> I find that doing so helps to keep my RAM requirements down a bit.
>>>> Perhaps that obvious/marginal suggestion might help for the time
>>>> being?
>>>
>>> Thanks. We have bits and pieces of a pipeline that do that. But we are
>> about
>>> to refactor that pipeline, so the hope is to make something that is
>> fairly
>>> clean, will endure, and handle the large objects that new sequencing
>>> technologies are likely to throw at us.
>>>
>>> Chuck
>>>>
>>>> -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<http://cbio.mskcc.org/%7Elianos/contact>
>>>>
>>>
>>> Charles C. Berry                            (858) 534-2098
>>>                                            Dept of Family/Preventive
>>> Medicine
>>> E mailto:cberry at tajo.ucsd.edu               UC San Diego
>>> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego
>> 92093-0901
>>>
>>>
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>>>
>>
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>

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