dyngen_estimation: Estimate Parameters From Real Datasets by dyngen

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

Estimate Parameters From Real Datasets by dyngen

Description

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

Usage

dyngen_estimation(ref_data, verbose = FALSE, other_prior, seed)

Arguments

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

Details

In dyngen, 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.

Value

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

References

Cannoodt R, Saelens W, Deconinck L, et al. Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells. Nature Communications, 2021, 12(1): 1-9. https://doi.org/10.1038/s41467-021-24152-2

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

Github URL: https://github.com/dynverse/dyngen

Examples

## Not run: 
ref_data <- simmethods::data

estimate_result <- simmethods::dyngen_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::dyngen_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.