Table of Contents

1. Get Started

1.1 Overview of MORGAN
1.2 Get the Tutorial
1.3 Get and set up the examples
1.4 Overview of the pedigrees used in the examples
1.5 Structure of the MORGAN package

2. Common Features and File Formats

2.1 Command syntax
2.2 Parameter file
2.3 File identification statements
2.4 Pedigree file
2.5 Pedigree file description statements

3. Checking Pedigree Validity

3.1 Introduction to pedcheck
3.2 Sample pedcheck parameter file
3.3 Running pedcheck examples
3.4 pedcheck statements

4. Computing Kinship and One- or Two-Locus Inbreeding Coefficients

4.1 Introduction to kin
4.2 Sample kin parameter file
4.3 Running kin example and sample output
4.4 kin statements

5. Simulating Marker and Trait Data in Pedigrees

5.1 Introduction to genedrop.
5.2 Sample genedrop parameter file
5.3 Running genedrop examples and sample output
5.4 genedrop statements

5.4.1 genedrop computing requests
5.4.2 genedrop mapping model parameters
5.4.3 genedrop population model parameters
5.4.4 genedrop computational parameters
5.4.5 genedrop output pedigree options
5.4.6 genedrop output seed file options

6. Simulating Marker Data Conditional on Trait Data in Pedigrees

6.1 Introduction to markerdrop
6.2 Sample markerdrop parameter file -- conditional on trait
6.3 Sample markerdrop parameter file -- conditional on inheritance pattern
6.4 Running markerdrop examples and sample output
6.5 markerdrop statements

6.5.1 markerdrop computing requests
6.5.2 markerdrop mapping model parameters
6.5.3 markerdrop population model parameters
6.5.4 markerdrop computational parameters
6.5.5 markerdrop input file options

7. Estimating a priori ibd Probabilities by Monte Carlo

7.1 Introduction to ibddrop
7.2 Sample ibddrop parameter file
7.3 Running ibddrop example and sample output
7.4 ibddrop statements

8. Using MCMC to Estimate Parameters of Interest in Pedigree Data

8.1 Specifying inheritance
8.2 Genetic model
8.3 Exact HMM computations
8.4 LM-sampler and LMM-sampler
8.5 MCMC parameters and options

9. Estimating Conditional ibd Probabilities by MCMC

9.1 Introduction to lm_auto and lm_pval
9.2 Sample lm_auto parameter file
9.3 Running lm_auto example and sample output
9.4 Sample lm_pval parameter file
9.5 Running lm_pval example and sample output
9.6 Autozyg statements

9.6.1 Autozyg computing requests
9.6.2 Autozyg file identification statements
9.6.3 Autozyg pedigree file description
9.6.4 Autozyg output file description
9.6.5 Autozyg mapping model parameters
9.6.6 Autozyg population model parameters
9.6.7 Autozyg computational parameters
9.6.8 Autozyg MCMC parameters and options

10. Estimating ibd Based Test Statistics by MCMC

10.1 Introduction to lm_ibdtests
10.2 Sample lm_ibdtests parameter file
10.3 Sample lm_ibdtests output
10.4 lm_ibdtests statements

11. Estimating Location LOD Scores by MCMC

11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell
11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell
11.3 Running lm_lods example and sample output
11.4 Running lm_markers examples and sample output
11.5 Running lm_bayes examples and sample output
11.6 Running lm_schnell example and sample output
11.7 Location LOD scores statements

11.7.1 Location LOD scores computing requests
11.7.2 Location LOD scores file identification statements
11.7.3 Location LOD scores pedigree file description
11.7.4 Location LOD scores output file description
11.7.5 Location LOD scores mapping model parameters
11.7.6 Location LOD scores population model parameters
11.7.7 Location LOD scores computational parameters
11.7.8 Location LOD scores MCMC parameters and options

12. Polygenic Modeling of Quantitative Traits by EM Algorithm

12.1 Introduction to PolyEM programs
12.2 Sample multivar parameter file
12.3 Running multivar example and sample output
12.4 multivar statements

12.4.1 multivar computing requests
12.4.2 multivar segregation model parameters
12.4.3 multivar computational parameters
12.4.4 multivar computational options
12.4.5 multivar output options

13. Estimating Genetic Map from Marker Data

13.1 Introduction to lm_map
13.2 Sample lm_map parameter file
13.3 Running lm_map with genotypic data
13.4 Running lm_map with phenotypic data
13.5 lm_map statements

Concept Index
Statement Index