VeloSim_simulation: Simulate Datasets by VeloSim

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

Simulate Datasets by VeloSim

Description

Simulate Datasets by VeloSim

Usage

VeloSim_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 and other variables are usually customed, so before simulating a dataset you must point it out.
return_format	A character. Alternatives choices: list, SingleCellExperiment, Seurat, h5ad
verbose	Logical. Whether to return messages or not.
seed	A random seed.

Details

In VeloSim, users can only set nCells and nGenes to specify the number of cells and genes in the simulated dataset. See Examples for instructions.

References

Zhang Z, Zhang X. VeloSim: Simulating single cell gene-expression and RNA velocity. BioRxiv, 2021. https://doi.org/10.1101/2021.01.11.426277

Github URL: https://github.com/PeterZZQ/VeloSim

Examples

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

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

# 1) Simulate with default parameters
simulate_result <- simmethods::VeloSim_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) 200 cells and 5000 genes
simulate_result <- simmethods::VeloSim_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = list(nCells = 200,
                     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.