splatPopEstimateMeanCV: Estimate gene mean and gene mean variance parameters

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

Estimate gene mean and gene mean variance parameters

Description

Estimate gene mean and gene mean variance parameters

Usage

splatPopEstimateMeanCV(params, emp.gene.means)

Arguments

params	SplatPopParams object containing parameters for the simulation of the mean expression levels for the population. See SplatPopParams for details.
emp.gene.means	data.frame of empirical gene means across a population, where rows are genes and columns are individuals.

Details

Parameters for the mean gamma distribution are estimated by fitting the mean (across the population) expression of genes that meet the criteria (<50 samples have exp <0.1) and parameters for the cv gamma distribution are estimated for each bin of mean expression using the cv of expression across the population for genes in that bin. Both are fit using fitdist. The "Nelder-Mead" method is used to fit the mean gamma distribution and the maximum goodness-of-fit estimation method is used to minimise the Cramer-von Mises distance for the CV distribution.

Value

params object with estimated values.

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