MORGAN V3.3.2 Tutorial

This is a tutorial for the MORGAN (Monte Carlo Genetic Analysis) package, focusing on how to use the provided programs.

The current version of this document is written for MORGAN Version 3.3.2.

The examples files in the text are updated.

The downloadable examples are current for MORGAN 3.3 (May 2015): in almost all cases the examples will run under MORGAN Version 3.3.2.

1. Get Started
2. Common Features and File Formats
3. Checking Pedigree Validity
4. Computing Kinship and Other Pedigree Computations
5. Simulating Marker and Trait Data in Pedigrees
6. Simulating Marker Data Conditional on Trait Data in Pedigrees
7. Estimating a priori ibd Probabilities by Monte Carlo
8. Using MCMC to Estimate Parameters of Interest in Pedigree Data
9. Estimating Conditional ibd Probabilities by MCMC
10. Estimating ibd Based Test Statistics by MCMC
11. Estimating Location lod Scores by MCMC
12. Population-based inference of IBD
13. Polygenic Modeling of Quantitative Traits by EM Algorithm
14. Estimating Genetic Maps from Marker Data
References
Concept Index
Statement Index