Write a H5AD file from a SingleCellExperiment object.
A SingleCellExperiment object.
String containing a path to write the new
Name of the assay to use as the primary matrix (
Logical scalar indicating whether assay matrices should
be ignored when writing to
skip_assays=TRUE can occasionally be useful if the matrices in
sce are stored in a format that is not amenable for efficient conversion
to a numpy-compatible format. In such cases, it can be better to create
an empty placeholder dataset in
file and fill it in R afterwards.
When first run, this function will instantiate a conda environment containing all of the necessary dependencies. This will not be performed on any subsequent run or if any other zellkonverter function has been run prior to this one.
The anndata package automatically converts some character vectors to
factors when saving
.h5ad files. This can effect columns of
colData(sce) which may change type when the
.h5ad file is read back
NULL is invisibly returned.
readH5AD(), to read a SingleCellExperiment file from a H5AD
SCE2AnnData(), for developers to create an AnnData object from a
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