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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
