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
