MendelKinship.jl

Julia utilities for computing theoretical/empirical kinship and other identity coefficients

MendelKinship.jl is a component of the umbrella OpenMendel project. Please read section on Kinship Comparison.

Package features

• Calculation of empirical and theoretical kinship coefficients, and their comparisons
• Approximation of Jacquard's 9 condensed identity coefficients via Monte Carlo gene dropping
• Calculation of Delta7 matrix for non-inbred pedigrees

For details, please read Chapter 5 of Mathematical and Statistical Methods for Genetic Analysis by Kenneth Lange, who wrote most of the code for this package.

Installation

Press ] to invoke the package manager mode and install the following:

add https://github.com/OpenMendel/SnpArrays.jl
add https://github.com/OpenMendel/MendelSearch.jl
add https://github.com/OpenMendel/MendelBase.jl
add https://github.com/OpenMendel/MendelKinship.jl

This package supports Julia v1.0+.

Manual Outline

• MendelKinship.jl
• Package features
• Installation
• Manual Outline
• Tutorial of MendelKinship
• Examples data
• Example 1: Theoretical Kinship Coefficient Calculation
• Example 2: Compare theoretical/empirical kinship values
• Interactive Plots and Tables
• Conclusions
• API
• Index
• Functions
• About
• When to use MendelKinship
• Using PLINK files as input
• Analysis keywords
• See also