[Bioc-devel] requirement for named assays in SummarizedExperiment

[Kasper Daniel Hansen]

allowing positional matching strikes me as being far too fragile.
Depending on the actual implementation, it may not even be clear there is
an order of the assays.

On Wed, Mar 11, 2015 at 2:45 PM, Valerie Obenchain <vobencha at fredhutch.org>
wrote:

> Hi,
>
> After talking with others the vote was against enforcing names on assays()
> and for positional matching if all names are NULL. A mixture of names and
> NULL throws an error.
>
> example(SummarizedExperiment)
>
> ## all named
> > se2 = se1
> > assays(cbind(se1, se2))
> List of length 1
> names(1): counts
>
> ## mixture of names and NULL -> error
> > names(assays(se1)) = NULL
> > assays(cbind(se1, se2))
> Error in assays(cbind(se1, se2)) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'assays': Error in .bind.arrays(args, cbind, "assays") :
>   elements in ‘assays’ must have the same names
>
> ## all NULL -> positional matching
> > names(assays(se2)) = NULL
> > assays(cbind(se1, se2))
> List of length 1
>
> If we find common use cases where positional matching is needed with a
> mixture of names and NULL we can always relax this constraint.
>
> Changes are in 1.19.46.
>
> Valerie
>
>
>
>
> On 03/06/2015 08:20 AM, Valerie Obenchain wrote:
>
>> Hi Aaron,
>>
>> Thanks for catching this.
>>
>> I favor enforcing names in 'assays'. Combining by position alone is too
>> dangerous. I'm thinking of the VCF class where the genome information is
>> stored in 'assays' and the fields are rarely in the same order.
>>
>> Looks like we also need a more informative error message when names
>> don't match.
>>
>>  > assays(se1)
>> List of length 1
>> names(1): counts1
>>
>>  > assays(se2)
>> List of length 1
>> names(1): counts2
>>
>>  > cbind(se1, se2)
>> Error in sQuote(accessorName) :
>>    argument "accessorName" is missing, with no default
>>
>>
>> Valerie
>>
>>
>> On 03/05/2015 11:09 PM, Aaron Lun wrote:
>>
>>> Dear all,
>>>
>>> I stumbled upon some unexpected behaviour with cbind'ing
>>> SummarizedExperiment objects with unnamed assays:
>>>
>>>  require(GenomicRanges)
>>>> nrows <- 5; ncols <- 4
>>>> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
>>>> rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
>>>> colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
>>>> sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
>>>> sset
>>>>
>>> class: SummarizedExperiment
>>> dim: 5 4
>>> exptData(0):
>>> assays(1): ''
>>> rownames: NULL
>>> rowData metadata column names(0):
>>> colnames(4): A B C D
>>> colData names(1): Treatment
>>>
>>>>
>>>> cbind(sset, sset)
>>>>
>>> dim: 5 8
>>> exptData(0):
>>> assays(0):
>>> rownames: NULL
>>> rowData metadata column names(0):
>>> colnames(8): A B ... C1 D1
>>> colData names(1): Treatment
>>>
>>> Upon cbind'ing, the assays in the SE object are lost. I think this is
>>> due to the fact that the cbind code matches up assays by their names.
>>> Thus, if there are no names, the code assumes that there are no assays.
>>>
>>> I guess this could be prevented by enforcing naming of assays in the
>>> SummarizedExperiment constructor. Or, the binding code could be modified
>>> to work positionally when there are no assay names, e.g., by cbind'ing
>>> the first assays across all SE objects, then the second assays, etc.
>>>
>>> Any thoughts?
>>>
>>> Regards,
>>>
>>> Aaron
>>>
>>>  sessionInfo()
>>>>
>>> R Under development (unstable) (2014-12-14 r67167)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4    parallel  stats     graphics  grDevices utils
>>> datasets
>>> [8] methods   base
>>>
>>> other attached packages:
>>> [1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
>>> [4] S4Vectors_0.5.21      BiocGenerics_0.13.6
>>>
>>> loaded via a namespace (and not attached):
>>> [1] XVector_0.7.4
>>>
>>>
>>> ______________________________________________________________________
>>> The information in this email is confidential and inte...{{dropped:15}}
>>>
>>
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>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, Seattle, WA 98109
>
> Email: vobencha at fredhutch.org
> Phone: (206) 667-3158
>
>
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