zinbwave_estimation: Estimate Parameters From Real Datasets by zinbwave

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

Estimate Parameters From Real Datasets by zinbwave

Description

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

Usage

zinbwave_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 zinbwave, users do not input other extra information usually. If users want to check the parameters, please see splatter::zinbEstimate() or splatter::ZINBParams().

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
## maybe it will take a long time
estimate_result <- simmethods::zinbwave_estimation(ref_data = ref_data,
                                                   other_prior = NULL,
                                                   verbose = TRUE,
                                                   seed = 111)

## End(Not run)

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