splatEstMean: Estimate Splat mean parameters

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

Estimate Splat mean parameters

Description

Estimate rate and shape parameters for the gamma distribution used to simulate gene expression means.

Usage

splatEstMean(norm.counts, params)

Arguments

norm.counts	library size normalised counts matrix.
params	SplatParams object to store estimated values in.

Details

Parameters for the gamma distribution are estimated by fitting the mean normalised counts using fitdist. The 'maximum goodness-of-fit estimation' method is used to minimise the Cramer-von Mises distance. This can fail in some situations, in which case the 'method of moments estimation' method is used instead. Prior to fitting the means are winsorized by setting the top and bottom 10 percent of values to the 10th and 90th percentiles.

Value

SplatParams object containing the estimated parameters.

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