TedSim_simulation: Simulate Datasets by TedSim

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

Simulate Datasets by TedSim

Description

Simulate Datasets by TedSim

Usage

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

Arguments

parameters	A object generated by TedSim_est()
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 TedSim, users can only set nGenes to specify the number of genes in the simulated dataset. See Examples for instructions.

References

Pan X, Li H, Zhang X. TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history. Nucleic acids research, 2022, 50(8): 4272-4288. https://doi.org/10.1093/nar/gkac235

Github URL: https://github.com/Galaxeee/TedSim

Examples

## Not run: 
ref_data <- simmethods::data

## estimation with cell group information
group_condition <- paste0("Group", as.numeric(simmethods::group_condition))
estimate_result <- simmethods::TedSim_estimation(
  ref_data = ref_data,
  other_prior = list(group.condition = group_condition),
  verbose = TRUE,
  seed = 111
)

# 1) Simulate with default parameters
simulate_result <- simmethods::TedSim_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)

# 2) 5000 genes
simulate_result <- simmethods::TedSim_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = list(nGenes = 5000),
  return_format = "list",
  verbose = TRUE,
  seed = 111
)

## counts
counts <- simulate_result[["simulate_result"]][["count_data"]]
dim(counts)

## End(Not run)

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