splatPopSimEffects {splatter} | R Documentation

## Add eQTL effects to means matrix

### Description

Add eQTL effects and non-eQTL group effects to simulated means matrix. The eQTL effects are incorporated using the following equation:

Ygs = (ESg x Mgs x Gs) + Mgs

Where Ygs is the mean for gene g and sample s, ESg is the effect size assigned to g, Mgs is the mean expression assigned to g for s, and Gs is the genotype (number of minor alleles) for s. Non-eQTL group effects are incorporated as:

Ygs = Mgs x GEg

Where GEg is the group effect (i.e. differential expression) assigned to g. To simulate multiple gene mean matrices with different group effects, this function can be run with 'id' designating the group id.

### Usage

    splatPopSimEffects(id, key, conditions, vcf, means.pop)

### Arguments

`id` | The group ID (e.g. "global" or "g1")
`key` | Partial splatPop key data.frame.
`conditions` | array of condition assignments for each sample
`vcf` | VariantAnnotation object containing genotypes of samples.
`means.pop` | Population mean gene expression matrix

### Value

data.frame of gene mean expression levels WITH eQTL effects.

[Package splatter version 1.18.2 Index]