generate: Generate data from regularized models.

In sctransform: Variance Stabilizing Transformations for Single Cell UMI Data

Generate data from regularized models.

Description

Generate data from regularized models. This generates data from the background, i.e. no residuals are added to the simulated data. The cell attributes for the generated cells are sampled from the input with replacement.

Usage

generate(
  vst_out,
  genes = rownames(vst_out$model_pars_fit),
  cell_attr = vst_out$cell_attr,
  n_cells = nrow(cell_attr)
)

Arguments

vst_out	A list that provides model parameters and optionally meta data; use output of vst function
genes	The gene names for which to generate data; default is rownames(vst_out$model_pars_fit)
cell_attr	Provide cell meta data holding latent data info; default is vst_out$cell_attr
n_cells	Number of cells to generate; default is nrow(cell_attr)

Value

Generated data as dgCMatrix

Examples

vst_out <- vst(pbmc, return_cell_attr = TRUE)
generated_data <- generate(vst_out)

sctransform documentation built on Oct. 19, 2023, 9:08 a.m.