CancerInSilico_simulation: Simulate Datasets by CancerInSilico

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

Simulate Datasets by CancerInSilico

Description

This function is used to simulate datasets from learned parameters by inSilicoGeneExpression function in CancerInSilico package.

Usage

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

Arguments

parameters	A object generated by CancerInSilico::calibratePathway()
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. Alternatives choices: list, SingleCellExperiment, Seurat, h5ad
verbose	Logical. Whether to return messages or not.
seed	A random seed.

Details

In CancerInSilico, users can only set nCells to specify the number of cells. See Examples. For more unusually used parameters in CancerInSilico, see CancerInSilico::inSilicoGeneExpression()

References

Sherman T D, Kagohara L T, Cao R, et al. CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS computational biology, 2019, 14(4): e1006935. https://doi.org/10.1371/journal.pcbi.1006935

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

Github URL: https://github.com/FertigLab/CancerInSilico

Examples

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

# 1) Simulate with default parameters
simulate_result <- simmethods::CancerInSilico_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) 2000 cells
simulate_result <- simmethods::CancerInSilico_simulation(
  parameters = estimate_result[["estimate_result"]],
  other_prior = list(nCells = 2000),
  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.