Lun2_estimation: Estimate Parameters From Real Datasets by Lun2

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

Estimate Parameters From Real Datasets by Lun2

Description

This function is used to estimate useful parameters from a real dataset by using lun2Estimate function in Splatter package.

Usage

Lun2_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

When you use Lun2 to estimate parameters from a real dataset, you must input a numeric vector to specify the batches or plates that each cell comes from, like ⁠other_prior = list(batch.condition = the numeric vector)⁠. See Examples and learn from it.

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
group_condition <- simmethods::group_condition
## group_condition can must be a numeric vector.
other_prior <- list(batch.condition = as.numeric(group_condition))
## Estimation
estimate_result <- simmethods::Lun2_estimation(ref_data = ref_data,
                                               other_prior = other_prior,
                                               verbose = TRUE,
                                               seed = 10)
estimate_result <- estimate_result[["estimate_result"]]
class(estimate_result) == "Lun2Params"

## End(Not run)

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