BASiCS_simulation: Simulate Datasets by BASiCS

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

Simulate Datasets by BASiCS

Description

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

Usage

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

Arguments

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

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

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