[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Michael Love]

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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