readH5AD: Read H5AD

In zellkonverter: Conversion Between scRNA-seq Objects

Description

Reads a H5AD file and returns a SingleCellExperiment object.

Usage

readH5AD(file, use_hdf5 = FALSE)

Arguments

file	String containing a path to a .h5ad file.
use_hdf5	Logical scalar indicating whether assays should be loaded as HDF5-based matrices from the HDF5Array package.

Details

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.

Value

A SingleCellExperiment object is returned.

Author(s)

Luke Zappia

Aaron Lun

See Also

writeH5AD(), to write a SingleCellExperiment object to a H5AD file.

AnnData2SCE(), for developers to convert existing AnnData instances to a SingleCellExperiment.

Examples

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))

zellkonverter documentation built on March 10, 2021, 2 a.m.