[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Vincent Carey stvjc at channing.harvard.edu
Sat Sep 20 16:38:33 CEST 2014

do we have a facility for this?

if not, we have



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
          if (any(isd <- duplicated(z[,"PROBEID"])))
     signIsStrand = TRUE,   # verify that signs of addresses define strand
     ucsdChrnames = TRUE    # prefix 'chr' to chromosome token

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