Subset Single Cell Experiment — subsetSCE • spacedeconv

Subset a SingleCellExperiment to reduce the number of cells

Usage

subsetSCE(
  sce,
  cell_type_col = "celltype_major",
  scenario = "even",
  ncells = 1000,
  notEnough = "asis",
  seed = 12345
)

Arguments

sce: SingleCellExperiment with cell type annotation
cell_type_col: name of colData column containing cell type information
scenario: which fraction of each celltype should be present in the subsampled dataset?
ncells: number of cells in total, defaults to 1000
notEnough: what to do if not enough cells are available c("remove", "asis")
seed: set a seed, enables reproducibility of subsetting step

Value

a singleCellExperiment with

Examples

data("single_cell_data_1")
sce <- subsetSCE(
  single_cell_data_1,
  cell_type_col = "celltype_major",
  scenario = "even",
  ncells = 100
)
#> ── spacedeconv ─────────────────────────────────────────────────────────────────
#> ℹ testing parameter
#> ℹ Set seed to 12345
#> ℹ testing parameter

#> ✔ parameter OK [28ms]
#> 
#> ℹ extracting up to 100 cells
#> ✔ extracting up to 100 cells [133ms]
#> 
#> ℹ extracted 96 cells
#> ✔ extracted 96 cells [22ms]
#>