I have just committed bsseq 0.9.4 to the devel branch of Biconductor. This update changes the underlying representation of objects of class 'BSseq' to use a SummarizedExperiment backend, and should make for a smoother ride when very large objects are manipulated. There are likely to be further updates in the coming days as potential bugs are found and removed (although it does pass all unitTests, all vignettes build and all examples run). Old serialized (saved) objects can be updated using x <- updateObject(x) Best, Kasper [[alternative HTML version deleted]]

This is terrific news! Combined with the more liberal constraints on matrices within assays() for SummarizedExperiments, an awful lot of infrastructure should be able to leverage them now. I'm going to play with some low-input-DNA BS-seq data this week, and am thrilled about the timing :-) Thanks, --t On Sat, Jul 6, 2013 at 2:35 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > I have just committed bsseq 0.9.4 to the devel branch of Biconductor. > > This update changes the underlying representation of objects of class > 'BSseq' to use a SummarizedExperiment backend, and should make for a > smoother ride when very large objects are manipulated. > > There are likely to be further updates in the coming days as potential bugs > are found and removed (although it does pass all unitTests, all vignettes > build and all examples run). > > Old serialized (saved) objects can be updated using > x <- updateObject(x) > > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]