splatPopEstimateEffectSize: Estimate eQTL Effect Size parameters
In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

splatPopEstimateEffectSize

R Documentation

Estimate eQTL Effect Size parameters

Description

Estimate rate and shape parameters for the gamma distribution used to simulate eQTL (eSNP-eGene) effect sizes.

Usage

splatPopEstimateEffectSize(params, eqtl)

Arguments

`params`	SplatPopParams object containing parameters for the simulation of the mean expression levels for the population. See `SplatPopParams` for details.
`eqtl`	data.frame with all or top eQTL pairs from a real eQTL analysis. Must include columns: gene_id, pval_nominal, and slope.

Details

Parameters for the gamma distribution are estimated by fitting the top eSNP- eGene pair effect sizes 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.