Kersplat_simulation: Simulate Datasets by Kersplat

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

Simulate Datasets by Kersplat

Description

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

Usage

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

Arguments

parameters	A object generated by splatter::kersplatEstimate()
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 and other variables 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 addtion to simulate datasets with default parameters, users can set two extra parameters before executing simulation step within Simple method:

1. nCells. Just only type other_prior = list(nCells = n) when you want to simulate a dataset with n cells.

2. nGenes. Like nCells, users just only type other_prior = list(nGenes = m) to get the dataset with m genes.

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 parameters
estimate_result <- Kersplat_estimation(ref_data = ref_data,
                                       verbose = TRUE,
                                       seed = 111)
# (1) Simulate a dataset with default parameters
simulate_result <- Kersplat_simulation(parameters = estimate_result[["estimate_result"]],
                                       return_format = "list",
                                       verbose = TRUE,
                                       seed = 111)
counts <- simulate_result[["simulate_result"]][["count_data"]]
dim(counts)

# (2) Simulate a dataset with customed number of cells and genes
simulate_result <- Kersplat_simulation(parameters = estimate_result[["estimate_result"]],
                                       return_format = "list",
                                       other_prior = list(nCells = 500,
                                                          nGenes = 3000),
                                       verbose = TRUE,
                                       seed = 111)
counts <- simulate_result[["simulate_result"]][["count_data"]]
dim(counts)

## End(Not run)

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