[Bioc-devel] SummarizedExperiments

[Kasper Daniel Hansen]

For extending SummarizedExperiments it would be convenient to have
something like Biobase::assayDataValidMembers

We might also consider putting Biobase::validMsg into BiocGenerics.

Kasper

On Fri, Sep 14, 2012 at 5:19 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 09/14/2012 11:46 AM, Kasper Daniel Hansen wrote:
>>
>> On Fri, Sep 14, 2012 at 2:25 PM, Tim Triche, Jr. <tim.triche at gmail.com>
>> wrote:
>>>
>>> For what it's worth I already wrote a CombineSEwithNAs() function to do
>>> this
>>> on the disjoint ranges for RRBS.  It assumes that there isn't any
>>> additional
>>> colData or elementMetadata of interest (for reasons that will become
>>> clear)
>>> and further assumes that the user will want to smooth.
>>
>>
>> I have one in bsseq as well (as I said earlier), but this would still
>> be nice to think about in the most general case possible.
>>
>>> seqlevels, seqlengths, genome are implemented via seqinfo as of the
>>> latest
>>> GenomicRanges package (went in some time ago, thanks to MM):
>>
>>
>> There is something I am missing here.  It clearly works.  But
>> showMethods("genome") tells me that methods are defined for Any,
>> Seqinfo, but if I use
>>    example(SummarizedExperiment)
>> to get sset defined, I still get
>>    is(sset, "Seqinfo")
>> to be FALSE.  I thought this would check for inheritance.
>
>
> The 'ANY' method on genome is implemented so that if you have a
> seqinfo,SummarizedExperiment-method, you get 'genome' for free. Another
> example is 'rownames' and 'colnames', which are provided for free when a
> dimnames,SummarizedExperiment-method is defined.
>
>> selectMethod("genome", "SummarizedExperiment")
> Method Definition:
>
> function (x)
> genome(seqinfo(x))
> <environment: namespace:GenomicRanges>
>
> Signatures:
>         x
> target  "SummarizedExperiment"
> defined "ANY"
>
> Martin
>
>
>>
>>> R> head(genome(LAML))
>>>    chr1  chr10  chr11  chr12  chr13  chr14
>>> "hg19" "hg19" "hg19" "hg19" "hg19" "hg19"
>>> R> head(seqlengths(LAML))
>>>       chr1     chr10     chr11     chr12     chr13     chr14
>>> 249250621 135534747 135006516 133851895 115169878 107349540
>>>
>>> I wrote a trivial addSeqinfo(x) function that, given a genome, will
>>> populate
>>> an SE's seqinfo automatically from a BSgenome (if there is one).  The
>>> function calls
>>>
>>> rtracklayer:::SeqinfoForBSGenome(unique(na.omit(genome(x))))[seqlevels(x)]
>>> to get the correct information.
>>>
>>> I hate the fact that there can be NA or differing genomes specified
>>> per-chromosome for SummarizedExperiments.  It makes me sad.
>>
>>
>> I don't like you can mix hg18/hg19 but on the other hand we routinely
>> spike in lambda phage and that is not really part of the human genome.
>>
>>>
>>>
>>>
>>> On Fri, Sep 14, 2012 at 10:54 AM, Kasper Daniel Hansen
>>> <kasperdanielhansen at gmail.com> wrote:
>>>>
>>>>
>>>> Thanks for all the additional methods.  I still miss
>>>>    seqlevels, seqlengths, genome
>>>>
>>>> Below,
>>>>
>>>> On Wed, Sep 12, 2012 at 3:33 PM, Martin Morgan <mtmorgan at fhcrc.org>
>>>> wrote:
>>>>>
>>>>> On 09/12/2012 12:15 PM, Kasper Daniel Hansen wrote:
>>>>
>>>>
>>>>>> One thing I have in my package that I find indispensable is combine
>>>>>> and (my own) combineList.  The later for combining > 2 objects, which
>>>>>> has a lot of possibilities for speed up especially if (very common)
>>>>>> all the objects have the same rowData, as opposed to Reduce(combine,
>>>>>> LIST)..  Usecase: you need to add additional samples to your
>>>>>> SummarizedExperiment.
>>>>>
>>>>>
>>>>>
>>>>> I found it difficult in Biobase to write combine methods for eSet,
>>>>> where
>>>>> you're really requiring a lot from the user (about the phenoData /
>>>>> featureData structured in the same way) or going through contortions to
>>>>> make
>>>>> it the same in a reasonable-but-ad-hoc way (e.g., when two columns are
>>>>> factors with the same set of levels but encoded differently). Maybe the
>>>>> effort required is proportional to the utility of the function
>>>>> provided...
>>>>> I'll give it some more thought.
>>>>
>>>>
>>>> In the abstract case it is hard to imagine combining different
>>>> SummarizedExperiments.  My usecase is almost always "additional
>>>> samples from the same experiment", and for that situation it is a lot
>>>> easier to imagine combining it.  You still need to check that the
>>>> granges are similar (and if not, expand some of the assayData with
>>>> zeroes or NA's), since the new samples may have coverage in locations
>>>> not assayed earlier.  Clearly factors are hard to handle and I assume
>>>> there are other hard to handle cases.  Nevertheless, I find such a
>>>> function incredibly useful.
>>>>
>>>> I think it is entirely ok to assume that the user knows what (s)he is
>>>> doing.
>>>>
>>>> Kasper
>>>
>>>
>>>
>>>
>>>
>>> --
>>> A model is a lie that helps you see the truth.
>>>
>>> Howard Skipper
>>>
>
>
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