SCRIP_estimation: Estimate Parameters From Real Datasets by SCRIP

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

Estimate Parameters From Real Datasets by SCRIP

Description

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

Usage

SCRIP_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

Qin F, Luo X, Xiao F, et al. SCRIP: an accurate simulator for single-cell RNA sequencing data. Bioinformatics, 2022, 38(5): 1304-1311. https://doi.org/10.1093/bioinformatics/btab824

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

Github URL: https://github.com/thecailab/SCRIP

Examples

## Not run: 
ref_data <- simmethods::data
estimate_result <- simmethods::SCRIP_estimation(ref_data = ref_data,
                                                verbose = TRUE,
                                                seed = 10)
estimate_result <- estimate_result[["estimate_result"]]
## Check the class (SCRIP accepts the estimation procedure in Splat)
class(estimate_result) == "SplatParams"

## End(Not run)

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