splatPopEstimateEffectSize: Estimate eQTL Effect Size parameters

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

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.

Value

params object with estimated values.

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