simpleEstimate: Estimate simple simulation parameters

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

Estimate simple simulation parameters

Description

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

Usage

simpleEstimate(counts, params = newSimpleParams())

## S3 method for class 'SingleCellExperiment'
simpleEstimate(counts, params = newSimpleParams())

## S3 method for class 'matrix'
simpleEstimate(counts, params = newSimpleParams())

Arguments

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

Details

The nGenes and nCells parameters are taken from the size of the input data. The mean parameters are estimated by fitting a gamma distribution to the library size normalised mean expression level using fitdist. See SimpleParams for more details on the parameters.

Value

SimpleParams object containing the estimated parameters.

Examples

# Load example data
library(scuttle)
set.seed(1)
sce <- mockSCE()

params <- simpleEstimate(sce)
params

Oshlack/splatter documentation built on Nov. 15, 2024, 7:25 p.m.