splatPopEstimateEffectSize {splatter} | 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.

### Value

params object with estimated values.

[Package splatter version 1.14.1 Index]