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? 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
