[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Hector Corrada Bravo]

Would be very useful in epivizr. Right now we have a little bit of code
that can be made much more general:
https://github.com/epiviz/epivizr/blob/master/R/register-methods.R#L73


On Sat, Sep 20, 2014 at 5:19 PM, Michael Love <michaelisaiahlove at gmail.com>
wrote:

> On Sep 20, 2014 2:15 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:
> >
> > 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'; 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.
> >
>
> Andrzej was working on a  conversion function for  DESeqDataSet <=>
> DGEList. I don't think it was for SummarizedExperiment and eSet.
>
> Mike
>
> > 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
> >>>
> >>>          [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
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> >>
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> >>
> >
> >
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