Select Page

# Documentation

Phenotype Simulation

## Description

Warning: Javascript is disabled. Equations will not be displayed properly.
DISSECT can simulate binary or quantitative traits by assuming they are caused from the additive effects of an arbitrary number of causant loci. Therefore, phenotype $$y_i$$ for individual i is computed as follows:

$y_i=g_i+e_i$ where $g_i=\sum_{k=1}^{N}{w_{ik}u_{k}}$

and

$w_{ik}=\frac{ \left(s_{ik} – 2p_k\right) }{ \sqrt{2p_k\left(1-p_k\right)} }$$$s_{ik}$$ is the number of copies of the reference allele for the SNP k of the individual i, $$p_k$$ is the frequency of the reference allele for the SNP k and N is the number of SNPs. $$u_{k}$$ is the effect of SNP k. $$e_{i}$$ is a random normal distributed variable centered at 0 and with a variance defined by the heritability and $$g_{i}$$ variance. Binary traits are simulated as quantitative traits, then individuals are classified as cases or controls. Cases will be those $$y_i$$ above a threshold and controls those with $$y_i$$ below this threshold. The threshold position is set based on chosen trait prevalence.

## Examples

Simulate a quantitative trait using SNPs (and effects if specified) in file snps.effects assuming a heritability of 0.2.

dissect --simulate --bfile genotypes --effect-sizes snps.effects --simu-h2 0.2 --simu-quantitative --out results

Simulate a binary trait using SNPs (and effects if specified) in file snps.effects assuming a heritability of 0.7 and a prevalence of 0.2.

dissect --simulate --bfile genotypes --effect-sizes snps.effects --simu-binary --simu-h2 0.7 --prevalence 0.2 --out results

## Options

#### Analysis Options

 --simulate Simulate phenotypes

#### Input Options

 --bfile f Specify a genotypes file. --bfile-list f Specify a file with a list of genotypes files. --effect-sizes f Specify the effect sizes file. It defines the causal SNPs an their effect size (if specified). More information in in http://www.dissect.ed.ac.uk/documentation-input-files/

#### Output Options

 --out f Specify the base name for output files.

#### Others

 --simu-quantitative Simulate quantitative trait. --simu-binary Simulate binary trait. --simu-h2 x Specify the heritability. --prevalence x Specify the prevalence.

## Output description

Three files are generated after a phenotypes simulation:

#### Phenotypes file

file extension: .simulated.phenos

This file contains the simulated phenotypes. File without header. Their columns are:

 Column 1 Family ID Column 2 Individual ID Cloumn 3 Simulated phenotypes

#### BLUPs file

file extension: .simulated.blups

This file contains the simulated BLUPs and the random effect. File without header.  Their coulmns are.

 Column 1 Family ID Column 2 Individual ID Cloumn 3 Simulated BLUPs Cloumn 4 Simulated environmental effect

#### SNP effects file

file extension: .simulated.effects

This file contains the SNPs effect sizes used in the simulations.

 Column 1 SNP name Column 2 Effect size.