SymSim_simulation: Simulate Datasets by SymSim

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

Simulate Datasets by SymSim

Description

Simulate Datasets by SymSim

Usage

SymSim_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 SymSim, 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 X, Xu C, Yosef N. Simulating multiple faceted variability in single cell RNA sequencing. Nature communications, 2019, 10(1): 1-16. https://doi.org/10.1038/s41467-019-10500-w

Github URL: https://github.com/YosefLab/SymSim

Examples

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

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

# 1) Simulate with default parameters
simulate_result <- simmethods::SymSim_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) 2000 cells and 5000 genes
simulate_result <- simmethods::SymSim_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = list(nCells = 2000,
                     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.