Re: [Bioc-devel] Empty DataFrame Causes SummarizedExperiment Constructor Error
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
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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Re: [Bioc-devel] Empty DataFrame Causes SummarizedExperiment Constructor Error
FWIW, it seems to me that the constructor expects the integrity between
the assay data and the column data. giving the correct row names,
there's no error:
SummarizedExperiment(assays = list(counts = countsMini), colData =
DataFrame(row.names=colnames(countsMini)))
class: SummarizedExperiment
dim: 10 10
metadata(0):
assays(1): counts
rownames(10): Gene 1 Gene 2 ... Gene 9 Gene 10
rowData names(0):
colnames(10): Cell 1 Cell 2 ... Cell 9 Cell 10
colData names(0):
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)
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
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--
Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
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Re: [Bioc-devel] Empty DataFrame Causes SummarizedExperiment Constructor Error
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
___
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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[Bioc-devel] Empty DataFrame Causes SummarizedExperiment Constructor Error
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
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