[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Martin Morgan]

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.

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]]
>>
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>
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>
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