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Load in a 10x CellRanger h5 file to SingleCells

load_tenx_h5.Rd

Loads the gene-expression modality from a CellRanger v2/v3 h5 file. The counts go into the Rust-binarised format (with log normalisation applied on read) and the barcodes/features into the DuckDB. Non-gene modalities (e.g. Antibody Capture) are filtered out via feature_type.

Usage

load_tenx_h5(
  object,
  h5_path,
  sc_qc_param = params_sc_min_quality(),
  feature_type = "Gene Expression",
  streaming = 1L,
  batch_size = 1000L,
  max_genes_in_memory = 2000L,
  cell_batch_size = 100000L,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

h5_path

File path to the 10x h5 file.

sc_qc_param

List. Output of params_sc_min_quality().

feature_type

String. Modality to keep. Defaults to "Gene Expression". Ignored for v2 (single modality).

streaming

Integer. CSR-to-CSC conversion mode. 0L -> in-memory, 1L -> light streaming, 2L -> heavy streaming. 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 information.

Examples

# read back a CellRanger v3 h5, gene expression only
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"
  )
)

dir_data <- tempfile("sc_tenx")
dir.create(dir_data, recursive = TRUE)
sc <- load_tenx_h5(
  object = SingleCells(dir_data = dir_data),
  h5_path = f_path,
  sc_qc_param = params_sc_min_quality(
    min_unique_genes = 5L,
    min_lib_size = 25L,
    min_cells = 5L
  ),
  streaming = 0L,
  .verbose = FALSE
)
dim(sc)
#> [1] 200  40

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