SymSim_estimation: Estimate Parameters From Real Datasets by SymSim

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

Estimate Parameters From Real Datasets by SymSim

Description

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

Usage

SymSim_estimation(ref_data, verbose = FALSE, other_prior = NULL, 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 SymSim, 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

Zhang X, Xu C, Yosef N. Simulating multiple faceted variability in single cell RNA sequencing. Nature communications, 2019, 10(1): 1-16. https://doi.org/10.1038/s41467-019-10500-w

Github URL: https://github.com/YosefLab/SymSim

Examples

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

estimate_result <- simmethods::SymSim_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::SymSim_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.