sctransform: generate – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

generate

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

Variance Stabilizing Transformations for Single Cell UMI Data

v0.3.2

GPL-3 | file LICENSE

Authors

Christoph Hafemeister [aut, cre] (<https://orcid.org/0000-0001-6365-8254>)

Initial release