[Bioc-devel] Empty DataFrame Causes SummarizedExperiment Constructor Error

[Hervé Pagès]

On 5/17/23 23:59, Robert Castelo wrote:

> not sure whether this is relevant, but I observed that while an empty 
> base R 'data.frame()' constructor gives zero-length character vectors 
> for row and column names, the empty 'DataFrame()' constructor gives 
> also a zero-length character vector for column names, but NULL for row 
> names, shouldn't this be consistent with base R 'data.frame()'?
>
> dimnames(data.frame())
> [[1]]
> character(0)
>
> [[2]]
> character(0)
>
> dimnames(DataFrame())
> [[1]]
> NULL
>
> [[2]]
> character(0)

This is a feature. Handling of the rownames of a DataFrame deviates from 
data.frame as documented in ?DataFrame.

H.

>
> robert.
>
> On 5/17/23 20:45, Hervé Pagès wrote:
>> Not sure why the colData default is DataFrame(). Seems like this has 
>> been the default since the birth of the SummarizedExperiment class 
>> back in 2010 (FWIW the class was born in the GenomicRanges package). 
>> Anyways, it should probably be NULL, like for rowData. Can you please 
>> open an issue on GitHub for this? Thanks
>>
>> H.
>>
>> On 5/12/23 07:00, Dario Strbenac via Bioc-devel wrote:
>>> Good day,
>>>
>>> The default value of colData is DataFrame(). Not specifying an 
>>> informative colData is fine.
>>>
>>> countsMini <- matrix(rpois(100, 100), ncol = 10)
>>> colnames(countsMini) <- paste("Cell", 1:10)
>>> rownames(countsMini) <- paste("Gene", 1:10)
>>> SummarizedExperiment(assays = list(counts = countsMini)) # Creates 
>>> the object successfully.
>>>
>>> But, explicitly specifying an empty DataFrame triggers an error. I 
>>> don't understand why it is not equivalent to the constructor's default.
>>>
>>> SummarizedExperiment(assays = list(counts = countsMini), colData = 
>>> DataFrame())
>>> Error in `rownames<-`(`*tmp*`, value = 
>>> .get_colnames_from_first_assay(assays)) :
>>>    invalid rownames length
>>>
>>> What is the subtle difference? It also seems like there could be a 
>>> clearer error message emitted if this is caught in the right place.
>>>
>>> --------------------------------------
>>> Dario Strbenac
>>> University of Sydney
>>> Camperdown NSW 2050
>>> Australia
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
-- 
Hervé Pagès

Bioconductor Core Team
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