On Wed, Mar 31, 2010 at 5:44 AM, David Rossell <
[email protected]> wrote:
> I see, thank you. One more thing, I haven't found any
> documentation/examples showing how one can set elementMetada and metadata
> (the section of the vignette is empty, the man files have no examples).
> Could you please point me to where this is explained?
>
>
I think class?Sequence explains it fairly well... IRanges could of course
benefit from many more examples..
> To use a simple example, say I have a RangedDataList with 4 elements, and I
> want to add the following phenotype information
>
> group: IP, IP, control, control
> batch: 1, 2, 1, 2
>
>
elementMetadata(rdl) <- DataFrame(group = c("IP", "IP", "control",
"control"), batch = c(1, 2, 1, 2))
Thanks!
>
> David
>
>
>
> On Wed, Mar 31, 2010 at 12:06 PM, Michael Lawrence <
> [email protected]> wrote:
>
>>
>>
>> On Wed, Mar 31, 2010 at 3:55 AM, David Rossell <
>> [email protected]> wrote:
>>
>>> Following a recent thread, I also have found convenient to store nextgen
>>> data as RangedData instead of ShortRead objects. They require far less
>>> memory and make feasible working with several samples at the same time
>>> (in
>>> my 8Gb RAM desktop I can load 2 ShortRead objects at the most, with
>>> RangedData I haven't struck the upper limit yet).
>>>
>>> I am thinking about taking this idea a step forward: RangedDataList
>>> allows
>>> storing info from several samples (e.g. IP and control) in a single
>>> object.
>>> The only problem is RangedDataList does not store information about the
>>> samples, e.g. the phenoData we're used to in ExpressionSet objects. My
>>> idea
>>> is to define something like a "SequenceSet" class, which would contain a
>>> RangedDataList with the ranges, a phenoData with sample information, and
>>> possibly also information about the experiment (e.g. with the MIAME
>>> analog
>>> for sequencing, MIASEQE).
>>>
>>> The thing is I don't want to re-invent the wheel. I haven't seen that
>>> this
>>> is implemented yet, but is someone working on it? Any criticism/ ideas?
>>>
>>>
>> RangedDataList already supports this. See the 'elementMetadata' and
>> 'metadata' slots in the Sequence class.
>>
>> Michael
>>
>>
>>
>>> Best,
>>>
>>> David
>>>
>>> --
>>> David Rossell, PhD
>>> Manager, Bioinformatics and Biostatistics unit
>>> IRB Barcelona
>>> Tel (+34) 93 402 0217
>>> Fax (+34) 93 402 0257
>>> http://www.irbbarcelona.org/bioinformatics
>>>
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>>>
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>>> Bioc-sig-sequencing mailing list
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>>>
>>
>>
>
>
> --
> David Rossell, PhD
> Manager, Bioinformatics and Biostatistics unit
> IRB Barcelona
> Tel (+34) 93 402 0217
> Fax (+34) 93 402 0257
> http://www.irbbarcelona.org/bioinformatics
>
>
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