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?
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
