TedSim_estimation: Estimate Parameters From Real Datasets by TedSim

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

Estimate Parameters From Real Datasets by TedSim

Description

This function is used to estimate useful parameters from a real dataset by using TedSim_est function in simmethods package.

Usage

TedSim_estimation(ref_data, other_prior = NULL, verbose = FALSE, seed)

Arguments

ref_data	A count matrix. Each row represents a gene and each column represents a cell.
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.
verbose	Logical.
seed	An integer of a random seed.

Details

In TedSim, users can input cell group information if it is available. If cell group information is not provided, the procedure will detect cell groups by kmeans automatically. See Examples for more instructions.

Note that TedSim can only simulate the dataset whose cell number is the power of 2 so if the reference data does not meet the requirement, the procedure will synthesize extra fake cells to achive this goal. See simutils::synthesize_cells() to learn about the process of synthesizing fake cells.

Value

A list contains the estimated parameters and the results of execution detection.

References

Pan X, Li H, Zhang X. TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history. Nucleic acids research, 2022, 50(8): 4272-4288. https://doi.org/10.1093/nar/gkac235

Github URL: https://github.com/Galaxeee/TedSim

Examples

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

## estimation with cell group information
group_condition <- paste0("Group", as.numeric(simmethods::group_condition))
estimate_result <- simmethods::TedSim_estimation(
  ref_data = ref_data,
  other_prior = list(group.condition = group_condition),
  verbose = TRUE,
  seed = 111
)

## End(Not run)

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