phenopath_simulation: Simulate Datasets by phenopath

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

Simulate Datasets by phenopath

Description

Simulate Datasets by phenopath

Usage

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

Arguments

parameters	A object generated by splatter::phenoEstimate()
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 phenopath, users can only set nCells and nGenes to specify the number of cells and genes in the simulated dataset. See Examples for instructions.

For more customed parameters, see splatter::PhenoParams() and splatter::phenoSimulate().

References

Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic and environmental backgrounds across single-cells and populations. bioRxiv, 2017: 159913. https://doi.org/10.1101/159913

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

Github URL: https://github.com/kieranrcampbell/phenopath

Examples

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

# 1) Simulate with default parameters
simulate_result <- simmethods::phenopath_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) 5000 cells and 6000 genes
simulate_result <- simmethods::phenopath_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = list(nCells = 5000,
                     nGenes = 6000),
  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.