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MORGAN V3.4 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 3.4.

Where the older examples for MORGAN 3.3 (May 2015) could be updated with minimal change, this has been done. These will be released and downloadable for MORGAN Version 3.4. In other cases, examples in the tutorial text are replaced by examples from the relevant program Gold standards.

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  
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This document was generated by Elizabeth Thompson on September 6, 2019 using texi2html 1.82.