dropsim_simulation: Simulate Datasets by dropsim

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

Simulate Datasets by dropsim

Description

This function is used to simulate datasets from learned parameters by simulateDGE function in dropsim package.

Usage

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

Arguments

parameters	A object generated by dropsim::fit_parameters()
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 dropsim, users can only set nCells and nGenes directly. For more parameters in dropsim, check dropsim::simulateDGE() and see Examples.

References

Github URL: https://github.com/marchinilab/dropsim

Examples

## Not run: 
ref_data <- simmethods::data
## estimation
estimate_result <- simmethods::dropsim_estimation(
  ref_data = ref_data,
  verbose = TRUE,
  seed = 111
)

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