Subsample from a sce object — subsample • PhiSpace

Subsample from a sce object

subsample(sce, key = NULL, proportion = 0.1, minCellNum = 50, seed = 5202056)

Arguments

sce: SCE object to be sampled from
key: Required for stratefied subsampling
proportion: Proportion of cells to sample
minCellNum: Minimum number of cells in each category
seed: Random seed. The function sets the seed with withr::local_seed(), so the session's random-number state is restored on exit.

Value

A downsized SCE object

Examples

sce <- scuttle::mockSCE(ncells = 200, ngenes = 10)
small <- subsample(sce, proportion = 0.2)
ncol(small)
# Stratified by a colData column, keeping at least 20 cells per class.
strat <- subsample(sce, key = "Cell_Cycle", proportion = 0.1, minCellNum = 20)
table(strat$Cell_Cycle)