Generate pseudo-bulked matrices — get_pseudobulked

This is a wrapper function to generate pseudo-bulked counts from a list of cell identifiers. You have the option to return sparse or dense matrices and if you wish to sum raw counts or calculate the mean of the normalised counts.

Usage

get_pseudobulked_sc(
  object,
  cell_list,
  return_format = c("dense", "sparse"),
  assay = c("raw", "norm"),
  .verbose = TRUE
)

Arguments

object: SingleCells or SingleCellsSubset class.
cell_list: Named list.
return_format: String. One of c("dense", "sparse").
assay: String. One of c("raw", "norm").
.verbose: Boolean or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

Pending on your setting in return_format a dense matrix or sparse CSR matrix with aggregated cells x genes.

Examples

# sum raw counts per planted cell type
sc <- demo_single_cells()
obs <- get_sc_obs(sc)
res <- get_pseudobulked_sc(
  sc,
  cell_list = split(obs$cell_id, obs$cell_grp),
  .verbose = FALSE
)
dim(res)
#> [1]  3 50

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