mfaEstimate: Estimate mfa simulation parameters

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

Estimate mfa simulation parameters

Description

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

Usage

mfaEstimate(counts, params = newMFAParams())

## S3 method for class 'SingleCellExperiment'
mfaEstimate(counts, params = newMFAParams())

## S3 method for class 'matrix'
mfaEstimate(counts, params = newMFAParams())

Arguments

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

Details

The nGenes and nCells parameters are taken from the size of the input data. The dropout lambda parameter is estimate using empirical_lambda. See MFAParams for more details on the parameters.

Value

MFAParams object containing the estimated parameters.

Examples

# Load example data
if (requireNamespace("mfa", quietly = TRUE)) {
    library(mfa)
    synth <- create_synthetic(
        C = 20, G = 5, zero_negative = TRUE,
        model_dropout = TRUE
    )

    params <- mfaEstimate(synth$X)
    params
}

Oshlack/splatter documentation built on April 1, 2024, 9:37 a.m.