SplatPop_estimation: Estimate Parameters From Real Datasets by SplatPop

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

Estimate Parameters From Real Datasets by SplatPop

Description

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

Usage

SplatPop_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 and other variables 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 estimating parameters with SplatPop, users can input some extra information (but it is rarely used):

1. means. Matrix of real gene means across a population, where each row is a gene and each column is an individual in the population.

2. eqtl. A data.frame with all or top eQTL pairs from a real eQTL analysis. Must include columns: 'gene_id', 'pval_nominal', and 'slope'. For more information, please check splatter::splatPopEstimate or https://www.bioconductor.org/packages/release/bioc/vignettes/splatter/inst/doc/splatPop.html

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
# Estimate parameters
estimate_result <- SplatPop_estimation(ref_data = ref_data,
                                       verbose = TRUE,
                                       seed = 111)
estimate_result <- estimate_result[["estimate_result"]]
## Check the class
class(estimate_result) == "SplatPopParams"

## End(Not run)

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