rliger (version 2.2.0)

readH5AD: Read matrix from H5AD file

Description

Read raw count matrix from H5AD file. By default, readH5AD load specified layer into memory (inMemory = TRUE). To use LIGER in delayed mode for handling large datasets, set inMemory = FALSE to load the data as a DelayedArray object. Note that only CSR format is supported for the matrix.

Usage

readH5AD(filename, layer, inMemory = TRUE, obs = FALSE)
readH5ADMem(filename, layer, obs = FALSE)
readH5ADDelay(filename, layer, obs = FALSE)

Value

When loaded in memory, a sparse matrix of class dgCMatrix will be returned. When loaded in delayed mode, a TENxMatrix object will be returned. If obs = TRUE, a list containing the matrix and the cell metadata will be returned.

Arguments

filename

Character string, path to the H5AD file.

layer

Character string specifying the H5 path of raw count data to be loaded. Use 'X' for adata.X, 'raw/X' for adata.raw.X, or 'layers/layer_name' for adata.layers['layer_name'].

inMemory

Logical, whether to load the data into memory. Default TRUE. FALSE loads the data as a DelayedArray object.

obs

Logical, whether to also load the cell metadata from adata.obs. Default FALSE.

Details

Currently, the only supported H5AD AnnData encoding versions are as follows:

• adata.X, adata.raw.X, or adata.layers['layer'] - csr_matrix 0.1.0

• adata.obs and adata.var - dataframe 0.2.0

• Categoricals in a data frame - categorical 0.2.0

If users possess H5AD files encoded with older specification, please either open an issue on GitHub or use R package 'anndata' to manually extract information.

Examples

tempH5AD <- tempfile(fileext = '.h5ad')
writeH5AD(pbmc, tempH5AD, overwrite = TRUE)
mat <- readH5AD(tempH5AD, layer = 'X')
delayMat <- readH5AD(tempH5AD, layer = 'X', inMemory = FALSE)