scDD_estimation: Estimate Parameters From Real Datasets by scDD

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

Estimate Parameters From Real Datasets by scDD

Description

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

Usage

scDD_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 scDD to estimate parameters from a real dataset, you must input a numeric vector to specify the groups or plates that each cell comes from, like ⁠other_prior = list(group.condition = the numeric vector)⁠. See Examples and learn from it.

Value

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

References

Korthauer K D, Chu L F, Newton M A, et al. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome biology, 2016, 17(1): 1-15. https://doi.org/10.1186/s13059-016-1077-y

Bioconductor URL: https://www.bioconductor.org/packages/release/bioc/html/scDD.html

Github URL: https://github.com/kdkorthauer/scDD

Examples

## Not run: 
ref_data <- SingleCellExperiment::counts(scater::mockSCE())
## group information
set.seed(111)
group_condition <- sample(c(1, 2), 200, replace = TRUE)
other_prior <- list(group.condition = group_condition)
## estimation
estimate_result <- simmethods::scDD_estimation(ref_data = ref_data,
                                               other_prior = other_prior,
                                               verbose = TRUE,
                                               seed = 111)

## End(Not run)

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