phenoEstimate: Estimate PhenoPath simulation parameters

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

Estimate PhenoPath simulation parameters

Description

Estimate simulation parameters for the PhenoPath simulation from a real dataset.

Usage

phenoEstimate(counts, params = newPhenoParams())

## S3 method for class 'SingleCellExperiment'
phenoEstimate(counts, params = newPhenoParams())

## S3 method for class 'matrix'
phenoEstimate(counts, params = newPhenoParams())

Arguments

counts	either a counts matrix or an SingleCellExperiment object containing count data to estimate parameters from.
params	PhenoParams object to store estimated values in.

Details

The nGenes and nCells parameters are taken from the size of the input data. The total number of genes is evenly divided into the four types. See PhenoParams for more details on the parameters.

Value

PhenoParams object containing the estimated parameters.

Examples

if (requireNamespace("phenopath", quietly = TRUE)) {
    # Load example data
    library(scuttle)
    set.seed(1)
    sce <- mockSCE()

    params <- phenoEstimate(sce)
    params
}

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.