kersplatEstimate: Estimate Kersplat simulation parameters

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

Estimate Kersplat simulation parameters

Description

Estimate simulation parameters for the Kersplat simulation from a real dataset. See the individual estimation functions for more details on how this is done.

Usage

kersplatEstimate(counts, params = newKersplatParams(), verbose = TRUE)

## S3 method for class 'SingleCellExperiment'
kersplatEstimate(counts, params = newKersplatParams(), verbose = TRUE)

## S3 method for class 'matrix'
kersplatEstimate(counts, params = newKersplatParams(), verbose = TRUE)

Arguments

counts	either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
params	KersplatParams object to store estimated values in.
verbose	logical. Whether to print progress messages.

Value

KersplatParams object containing the estimated parameters.

See Also

kersplatEstMean, kersplatEstBCV, kersplatEstLib

Examples

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

    params <- kersplatEstimate(sce)
    params
}

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