Would be very useful in epivizr. Right now we have a little bit of code that can be made much more general: https://github.com/epiviz/epivizr/blob/master/R/register-methods.R#L73
On Sat, Sep 20, 2014 at 5:19 PM, Michael Love <michaelisaiahl...@gmail.com> wrote: > On Sep 20, 2014 2:15 PM, "Martin Morgan" <mtmor...@fhcrc.org> wrote: > > > > On 09/20/2014 10:43 AM, Sean Davis wrote: > >> > >> Hi, Vince. > >> > >> Looks like a good start. I'd probably pull all the assays from > >> ExpressionSet into SummarizedExperiment as the default, avoiding data > >> coercion methods that are unnecessarily lossy. Also, as it stands, the > >> assayname argument is not used anyway? > > > > > > I think there will be some resistance to uniting the 'Biobase' and > 'IRanges' realms under 'GenomicRanges'; considerable effort has gone in to > making a rational hierarchy of package dependencies [perhaps Herve will > point to some of his ASCII art on the subject]. > > > > I have some recollection of (recent) discussion related to this topic in > the DESeq2 realm, but am drawing a blank; presumably Michael or Wolfgang or > ... will chime in. > > > > Andrzej was working on a conversion function for DESeqDataSet <=> > DGEList. I don't think it was for SummarizedExperiment and eSet. > > Mike > > > Martin > > > > > >> > >> Sean > >> > >> > >> On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey < > st...@channing.harvard.edu> > >> wrote: > >> > >>> do we have a facility for this? > >>> > >>> if not, we have > >>> > >>> https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R > >>> > >>> > https://github.com/vjcitn/biocMultiAssay/blob/master/man/coerce-methods.Rd > >>> > >>> it occurred to me that we might want something like this in > GenomicRanges > >>> (that's where SummarizedExperiment is managed, right?) and I will add > it > >>> if there are no objections > >>> > >>> the arguments are currently > >>> > >>> assayname = "exprs", # for naming SimpleList element > >>> fngetter = > >>> function(z) rownames(exprs(z)), # extract usable feature > names > >>> annDbGetter = > >>> function(z) { > >>> clnanno = sub(".db", "", annotation(z)) > >>> stopifnot(require(paste0(annotation(z), ".db"), > >>> character.only=TRUE) ) > >>> get(paste0(annotation(z), ".db")) # obtain resource for > >>> mapping feature names to coordinates > >>> }, > >>> probekeytype = "PROBEID", # chipDb field to use > >>> duphandler = function(z) { # action to take to process > duplicated > >>> features > >>> if (any(isd <- duplicated(z[,"PROBEID"]))) > >>> return(z[!isd,,drop=FALSE]) > >>> z > >>> }, > >>> signIsStrand = TRUE, # verify that signs of addresses define > strand > >>> ucsdChrnames = TRUE # prefix 'chr' to chromosome token > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioc-devel@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > -- > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 > > > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
