dyngen_simulation: Simulate Datasets by dyngen

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

Simulate Datasets by dyngen

Description

Simulate Datasets by dyngen

Usage

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

Arguments

parameters	A object generated by infer_trajectory
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 dyngen, users can only set nCells and nGenes to specify the number of cells and genes in the simulated dataset. See Examples for instructions.

References

Cannoodt R, Saelens W, Deconinck L, et al. Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells. Nature Communications, 2021, 12(1): 1-9. https://doi.org/10.1038/s41467-021-24152-2

CRAN URL: https://cran.r-project.org/web/packages/dyngen/index.html

Github URL: https://github.com/dynverse/dyngen

Examples

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

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

# 1) Simulate with default parameters (need a lot of memory)
simulate_result <- simmethods::dyngen_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) 100 cells and 100 genes
simulate_result <- simmethods::dyngen_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = list(nCells = 100,
                     nGenes = 100),
  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.