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Stream in h5ad to SingleCells

stream_h5ad.Rd

This function takes an h5ad file and loads (via streaming) the obs and var data into the DuckDB of the SingleCells class and the counts into a Rust-binarised format for rapid access. During the reading in of the counts, the log CPM transformation will occur automatically. This function is specifically designed to deal with larger amounts of data and is slower than load_h5ad().

Usage

stream_h5ad(
  object,
  h5_path,
  sc_qc_param = params_sc_min_quality(),
  max_genes_in_memory = 2000L,
  cell_batch_size = 100000L,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

h5_path

File path to the h5ad object you wish to load in.

sc_qc_param

List. Output of params_sc_min_quality(). A list with the following elements:

  • min_unique_genes - Integer. Minimum number of genes to be detected in the cell to be included.

  • min_lib_size - Integer. Minimum library size in the cell to be included.

  • min_cells - Integer. Minimum number of cells a gene needs to be detected to be included.

  • target_size - Float. Target size to normalise to. Defaults to 1e5.

max_genes_in_memory

Integer. How many genes shall be held in memory at a given point. Defaults to 2000L.

cell_batch_size

Integer. How big are the batch sizes for the cells in the transformation from the cell-based to gene-based format. Defaults to 100000L.

.verbose

Boolean. Controls the verbosity of the function.

Value

It will populate the files on disk and return the class with updated shape information.