Helper function to write data to a 10x CellRanger-style h5 file

Usage

write_tenx_h5_sc(
  f_path,
  counts,
  barcodes,
  features,
  version = c("v3", "v2"),
  overwrite = TRUE
)

Arguments

f_path: String. Output path.
counts: Sparse matrix (dgRMatrix or dgCMatrix), cells x features.
barcodes: Character. Cell barcodes, length nrow(counts).
features: data.table with id and name of length ncol(counts). For v3 may include feature_type; defaults to "Gene Expression" if absent.
version: One of "v3" or "v2".
overwrite: Boolean.

Value

Invisible.

Examples

# a CellRanger v3 style h5, ready for load_tenx_h5()
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$ensembl_id
  )
)
read_tenx_h5_metadata(f_path)$dims
#> obs var 
#> 200  40 

unlink(f_path)