[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Vincent Carey]

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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