splatEstBCV: Estimate Splat Biological Coefficient of Variation parameters

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

Estimate Splat Biological Coefficient of Variation parameters

Description

Parameters are estimated using the estimateDisp function in the edgeR package.

Usage

splatEstBCV(counts, params)

Arguments

counts	counts matrix to estimate parameters from.
params	SplatParams object to store estimated values in.

Details

The estimateDisp function is used to estimate the common dispersion and prior degrees of freedom. See estimateDisp for details. When estimating parameters on simulated data we found a broadly linear relationship between the true underlying common dispersion and the edgR estimate, therefore we apply a small correction, disp = 0.1 + 0.25 * edgeR.disp.

Value

SplatParams object with estimated values.

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