hierarchicell_estimation: Estimate Parameters From Real Datasets by hierarchicell

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

Estimate Parameters From Real Datasets by hierarchicell

Description

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

Usage

hierarchicell_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. For more customed parameters, see hierarchicell::compute_data_summaries()
seed	An integer of a random seed.

Value

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

References

Zimmerman K D, Langefeld C D. Hierarchicell: an R-package for estimating power for tests of differential expression with single-cell data. BMC genomics, 2021, 22(1): 1-8. https://doi.org/10.1186/s12864-021-07635-w

Github URL: https://github.com/kdzimm/hierarchicell

Examples

## Not run: 
ref_data <- SingleCellExperiment::counts(scater::mockSCE())
## estimation
estimate_result <- simmethods::hierarchicell_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.