BASiCS_estimation: Estimate Parameters From Real Datasets by BASiCS

View source: R/17-BASiCS.R

BASiCS_estimationR Documentation

Estimate Parameters From Real Datasets by BASiCS

Description

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

Usage

BASiCS_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.

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


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