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Generate `scbench` object

Usage

new_scbench(
  ref_scrna,
  annot_ids,
  pop_bounds = NULL,
  project_name = "project",
  cache_path = "scbench_cache",
  batch_id = NULL
)

Arguments

ref_scrna

a reference Seurat object

annot_ids

named vector with column names of annotations per level, e.g. `c("l1" = "annot1", "l2" = "annot2")`

pop_bounds

list of population bounds, see example. If `NULL`, bounds will be set to 0-1 for every population.

project_name

a string indicating the project name, used for caching

cache_path

path to the directory where results will be cached

batch_id

NULL or a string of a column name with the batch information for simulating pseudobulks by batch

Value

an object of class scbench