splatPopSimEffects: Add eQTL effects to means matrix

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

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.

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