Works like a charm, thank you. Just for the record, I did look at the man pages (RangedDataSet, Sequence etc) but could not figure out how to solve this simple situation. An example either in the man or the vignette would help newcomers enormously. :-)
David On Wed, Mar 31, 2010 at 1:54 PM, Michael Lawrence <[email protected] > wrote: > > > 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 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-sig-sequencing mailing list >>>> [email protected] >>>> 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 >> >> > -- 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
