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Read obs and var tables and metadata from an h5ad file

read_h5ad_metadata.Rd

Useful for exploring the data stored in an h5ad file.

Usage

read_h5ad_metadata(f_path)

Arguments

f_path

File path to the .h5ad file.

Value

A list with:

  • obs - data.table of cell-level metadata

  • var - data.table of gene-level metadata

  • dims - named integer vector c(obs, var)

  • type - "CSR" or "CSC"

Examples

# obs and var tables straight out of the file
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$var, .verbose = FALSE)
meta <- read_h5ad_metadata(f_path)
head(meta$var, 3)
#>        .id ensembl_id
#>     <char>     <char>
#> 1: gene_01     ens_01
#> 2: gene_02     ens_02
#> 3: gene_03     ens_03

unlink(f_path)