[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Hi,
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';
This coercion method could be defined (1) in Biobase (where
ExpressionSet is defined), (2) in GenomicRanges (where
SummarizedExperiment is defined), or (3) in a package that
depends on Biobase and GenomicRanges.

Since it's probably undesirable to make Biobase depend on GenomicRanges
or vice-versa, we would need to use Suggests for (1) or (2). That
means we would get a note like this at installation time:

  ** preparing package for lazy loading
  in method for ?coerce? with signature 
?"ExpressionSet","SummarizedExperiment"?:
  no definition for class ?SummarizedExperiment?

Not very clean but it works.

(3) is a cleaner solution but then the coercion method would
not necessarily be available to the user when s/he needs it (unless
s/he knows what extra package to load). The obvious advantage of
putting the method in Biobase is that if a user has an ExpressionSet,
then s/he necessarily has Biobase attached and the method is already
in her/his search path.

Another solution would be (4) to move SummarizedExperiment somewhere
else. That would be in a package that depends on GenomicRanges and
Biobase, and the coercion method would be defined there.

H.
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.

Martin

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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[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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