Helper function to write data to h5ad format

This is a helper to write synthetic data to h5ad file. This version will write the data into the common compressed sparse data format.

Usage

write_h5ad_sc(f_path, counts, obs, var, overwrite = TRUE, .verbose = TRUE)

Arguments

f_path

String. The filepath to which to save the data

counts

Sparse matrix. Needs to be of class dgRMatrix or dgCMatrix.

obs

data.table. The observations. Needs to have nrow(obs) == nrow(counts).

var

data.table. The variable data. Needs to have ncol(var) == ncol(counts).

overwrite

Boolean. Shall any found h5ad file be overwritten.

.verbose

Boolean. Controls verbosity of the function.

Value

Returns invisible

Examples

# round trip synthetic counts through a sparse h5ad
data <- generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(n_cells = 200L, n_genes = 40L)
)
f_path <- tempfile(fileext = ".h5ad")
write_h5ad_sc(f_path, data$counts, data$obs, data$var, .verbose = FALSE)
get_h5ad_dimensions(f_path)$dims
#> obs var 
#> 200  40 

unlink(f_path)