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Read barcode and feature tables and metadata from a 10x h5 file

read_tenx_h5_metadata.Rd

Useful for exploring the data stored in a 10x CellRanger v2/v3 h5 file, including the breakdown of feature types in a multi-modal file.

Usage

read_tenx_h5_metadata(f_path)

Arguments

f_path

File path to the 10x .h5 file.

Value

A list with:

  • obs - data.table of barcodes

  • var - data.table of features (id, name, and feature_type for v3)

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

  • version - "v2" or "v3"

  • feature_types - named integer vector of feature_type counts (v3 only, otherwise NULL)

Examples

# barcodes, features and the feature type breakdown
data <- generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(n_cells = 200L, n_genes = 40L)
)
f_path <- tempfile(fileext = ".h5")
write_tenx_h5_sc(
  f_path = f_path,
  counts = data$counts,
  barcodes = data$obs$cell_id,
  features = data.table::data.table(
    id = data$var$gene_id,
    name = data$var$ensembl_id,
    feature_type = "Gene Expression"
  )
)
meta <- read_tenx_h5_metadata(f_path)
meta$dims
#> obs var 
#> 200  40 
meta$feature_types
#> Gene Expression 
#>              40 

unlink(f_path)