Documentation

Description

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.