zinbwave_simulation: Simulate Datasets by zinbwave

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

Simulate Datasets by zinbwave

Description

This function is used to simulate datasets from learned parameters by zinbSimulate function in Splatter package.

Usage

zinbwave_simulation(parameters, return_format, verbose = FALSE, seed)

Arguments

parameters	A object generated by splatter::zinbEstimate()
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.

References

Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA sequencing data. Genome biology, 2017, 18(1): 1-15. https://doi.org/10.1186/s13059-017-1305-0

Bioconductor URL: https://bioconductor.org/packages/release/bioc/html/splatter.html

Github URL: https://github.com/Oshlack/splatter

Examples

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

estimate_result <- simmethods::zinbwave_estimation(ref_data = ref_data,
                                                   other_prior = NULL,
                                                   verbose = TRUE,
                                                   seed = 111)

## In zinbwave, users can not set the number of cells and genes.
simulate_result <- simmethods::zinbwave_simulation(
  parameters = estimate_result[["estimate_result"]],
  return_format = "list",
  verbose = TRUE,
  seed = 111
)

## End(Not run)

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