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,
  modality = c("rna", "adt"),
  .verbose = TRUE
)

Arguments

object: SingleCells, MetaCells, SingleCellsMultiModal 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.
modality: String. The modality to return. One of c("rna", "adt").
.verbose: Boolean. Controls verbosity of the function.

Value

The counts table

Examples

# raw counts for the first ten genes, cell-centric (CSR)
sc <- demo_single_cells(prepped = FALSE)
counts <- get_sc_counts(sc, gene_indices = 1:10, .verbose = FALSE)
dim(counts)
#> [1] 500  10

unlink(sc@dir_data, recursive = TRUE, force = TRUE)