scMultiSim_simulation: Simulate Datasets by scMultiSim

In duohongrui/simmethods: A collection of 40+ simulation methods for singlce-cell RNA seqencing data

Simulate Datasets by scMultiSim

Description

Simulate Datasets by scMultiSim

Usage

scMultiSim_simulation(
  parameters,
  other_prior = NULL,
  return_format,
  verbose = FALSE,
  seed
)

Arguments

parameters	A object generated by simutils::make_trees()
other_prior	A list with names of certain parameters. Some methods need extra parameters to execute the estimation step, so you must input them. In simulation step, the number of cells, genes, groups, batches, the percent of DEGs are usually customed, so before simulating a dataset you must point it out. See Details below for more information.
return_format	A character. Alternative choices: list, SingleCellExperiment, Seurat, h5ad. If you select h5ad, you will get a path where the .h5ad file saves to.
verbose	Logical. Whether to return messages or not.
seed	A random seed.

Details

In scMultiSim, nCells and nGenes are usually customed and users can set other_prior = list(nCells = 1000, nGenes = 2000) to simulate 1000 cells and 5000 genes. In addition, nBatches can be customed for simulating the cell batches.

References

Li H, Zhang Z, Squires M, et al. scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks. bioRxiv, 2022: 2022.10. 15.512320. https://doi.org/10.1101/2022.10.15.512320

Github URL: https://github.com/ZhangLabGT/scMultiSim

Examples

ref_data <- simmethods::data
## estimation
estimate_result <- simmethods::scMultiSim_estimation(
  ref_data = ref_data,
  other_prior = NULL,
  verbose = TRUE,
  seed = 111
)

# 1) Simulate with default parameters
simulate_result <- simmethods::scMultiSim_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = NULL,
  return_format = "list",
  verbose = TRUE,
  seed = 111
)
## counts
counts <- simulate_result[["simulate_result"]][["count_data"]]
dim(counts)

duohongrui/simmethods documentation built on June 17, 2024, 10:49 a.m.