Getter the counts — get_sc_counts • bixverse

Getter the counts

Usage

get_sc_counts(
  object,
  assay = c("raw", "norm"),
  return_format = c("cell", "gene"),
  cell_indices = NULL,
  gene_indices = NULL,
  use_cells_to_keep = TRUE,
  .verbose = TRUE
)

Arguments

object: SingleCells, MetaCells class.
assay: String. Which slot to return. One of c("raw", "norm"). Defaults to "raw".
return_format: String. One of c("cell", "gene"). Return data in cell-centric compressed format (CSR) or gene-centric compressed format (CSC). Defaults to "cell". Not relevant for MetaCells.
cell_indices: Optional cell indices.
gene_indices: Optional gene indices.
use_cells_to_keep: Boolean. Shall cells to keep be found in the class, shall the counts be reduced to these. Not relevant for MetaCells.
.verbose: Boolean. Controls verbosity of the function.

Value

The counts table