Skip to contents

Load multiple h5ad files into a single SingleCells

load_multi_h5ad.Rd

Takes a pre-scan result from prescan_h5ad_files() and loads all files into a single experiment with global gene QC and sequential cell indexing.

Usage

load_multi_h5ad(
  object,
  prescan_result,
  sc_qc_param = params_sc_min_quality(),
  cell_id_col = NULL,
  streaming = 1L,
  batch_size = 1000L,
  max_genes_in_memory = 2000L,
  cell_batch_size = 100000L,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

prescan_result

Output of prescan_h5ad_files().

sc_qc_param

List. Output of params_sc_min_quality().

cell_id_col

Optional string. Column name for cell identifiers in obs.

streaming

Integer. 0L -> in-memory, 1L -> light streaming, 2L -> heavy streaming with memory upper boundaries. Defaults to 1L.

batch_size

Integer. Cell batch size when streaming = 1L. Defaults to 1000L.

max_genes_in_memory

Integer. Maximum genes held in memory at once when streaming = 2L. Defaults to 2000L.

cell_batch_size

Integer. Cell batch size when streaming = 2L. Defaults to 100000L.

.verbose

Boolean.

Value

The class with updated shape and populated DuckDB.

Examples

# two files into one experiment, cells tagged by exp_id
files <- c(a = tempfile(fileext = ".h5ad"), b = tempfile(fileext = ".h5ad"))
for (i in seq_along(files)) {
  data <- generate_single_cell_test_data(
    syn_data_params = params_sc_synthetic_data(
      n_cells = 200L,
      n_genes = 40L
    ),
    seed = i
  )
  write_h5ad_sc(files[i], data$counts, data$obs, data$var, .verbose = FALSE)
}
tasks <- prescan_h5ad_files(h5_paths = files, .verbose = FALSE)
dir_data <- tempfile("sc_multi_h5ad")
dir.create(dir_data, recursive = TRUE)
sc <- load_multi_h5ad(
  object = SingleCells(dir_data = dir_data),
  prescan_result = tasks,
  sc_qc_param = params_sc_min_quality(
    min_unique_genes = 5L,
    min_lib_size = 25L,
    min_cells = 5L
  ),
  streaming = 0L,
  .verbose = FALSE
)
table(sc[["exp_id"]])
#> exp_id
#>   a   b 
#> 200 200 

unlink(c(files, dir_data), recursive = TRUE, force = TRUE)