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
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:
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
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))
