readH5AD {zellkonverter} | R Documentation |
Reads a H5AD file and returns a SingleCellExperiment object.
readH5AD(file, X_name = NULL, use_hdf5 = FALSE, reader = c("python", "R"))
file |
String containing a path to a |
X_name |
Name used when saving |
use_hdf5 |
Logical scalar indicating whether assays should be loaded as HDF5-based matrices from the HDF5Array package. |
reader |
Which HDF5 reader to use. Either |
Setting use_hdf5 = TRUE
allows for very large datasets to be efficiently
represented on machines with little memory. However, this comes at the cost
of access speed as data needs to be fetched from the HDF5 file upon request.
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.
Setting reader = "R"
will use an experimental native R reader instead of
reading the file into Python and converting the result. This avoids the need
for a Python environment and some of the issues with conversion but is still
under development and is likely to return slightly different output.
A SingleCellExperiment object is returned.
Luke Zappia
Aaron Lun
writeH5AD()
, to write a SingleCellExperiment object to a
H5AD file.
AnnData2SCE()
, for developers to convert existing AnnData instances to a
SingleCellExperiment.
library(SummarizedExperiment) file <- system.file("extdata", "krumsiek11.h5ad", package = "zellkonverter") sce <- readH5AD(file) class(assay(sce)) sce2 <- readH5AD(file, use_hdf5 = TRUE) class(assay(sce2)) sce3 <- readH5AD(file, reader = "R")