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?

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

Thanks!

David


On Wed, Mar 31, 2010 at 12:06 PM, Michael Lawrence <
lawrence.michael@gene.com> wrote:

>
>
> On Wed, Mar 31, 2010 at 3:55 AM, David Rossell <
> david.rossell@irbbarcelona.org> 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@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>
>


-- 
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

	[[alternative HTML version deleted]]

