SRTsim_simulation: Simulate Datasets by SRTsim

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

Simulate Datasets by SRTsim

Description

This function is used to simulate datasets from learned parameters by srtsim_count function in SRTsim package.

Usage

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

Arguments

parameters	A object generated by SRTsim::srtsim_fit()
other_prior	A list with names of certain parameters in SRTsim.
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

For more customed parameters in SRTsim, please check SRTsim::srtsim_fit(). For detailed information about SRTsim, go to https://cran.r-project.org/web/packages/SRTsim/index.html.

References

Zhu J, Shang L, Zhou X. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics. Genome Biology, 2023, 24(1): 39. https://doi.org/10.1186/s13059-023-02879-z

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

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