Simple_estimation: Estimate Parameters From Real Datasets by Simple

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

Estimate Parameters From Real Datasets by Simple

Description

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

Usage

Simple_estimation(ref_data, verbose = FALSE, seed)

Arguments

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

Value

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

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 <- Simple_estimation(ref_data = ref_data,
                                     verbose = TRUE,
                                     seed = 111)
estimate_result <- estimate_result[["estimate_result"]]
## Check the class
class(estimate_result) == "SimpleParams"

## End(Not run)

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