[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Sean Davis]

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 <stvjc at 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
>
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