Generate pseudobulk gene expression from single-cell RNA-seq given population mixtures in an `scbench` object

Generate pseudobulk gene expression from single-cell RNA-seq given population mixtures in an `scbench` object

Usage

pseudobulks(
  scbench,
  ncells = 2000,
  spatial_ncells = 30,
  ncores = 8,
  shrink_obj = TRUE,
  by_batch = FALSE,
  seed = 0
)

Arguments

scbench

an `scbench` object that has been evaluated by `population_mixtures`

ncells

an integer, the number of cells to pool into pseudobulk.

shrink_obj

a boolean, if TRUE, `scbench` object is reduced in size by removing the single-cell expression data and keeping only its metadata after estimating the pseudobulks

by_batch

a boolean, if TRUE, pseudobulks are estimated by batch using the `batch_id` provided when creating the object.

seed

an integer representing a "seed", for reproducibility of mixtures.

level

a string character, the reference data level for pseudobulk pooling (e.g. `"l1"`, `"l2"`)

Value

an object of class `scbench`