| Index Entry | Section |
|---|
|
| K | | |
|---|
| kin introduction | 4.1 Introduction to kin |
| kin sample output | 4.3 Running kin example and sample output |
| kin sample parameter file | 4.2 Sample kin parameter file |
| kin statements | 4.4 kin statements |
| kinship coefficient | 4.1 Introduction to kin |
| kinship coefficient | 4.4 kin statements |
| Kosambi map function | 5.4.2 genedrop mapping model parameters |
| Kosambi map function | 6.5.2 markerdrop mapping model parameters |
| Kosambi map function | 6.5.2 markerdrop mapping model parameters |
| Kosambi map function | 11.7.5 Location LOD scores mapping model parameters |
|
| L | | |
|---|
| L-sampler | 8.4 LM-sampler and LMM-sampler |
| L-sampler | 9.2 Sample lm_auto parameter file |
| L-sampler | 9.6.8 Autozyg MCMC parameters and options |
| L-sampler | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| L-sampler probability | 8.4 LM-sampler and LMM-sampler |
| LM-sampler | 8.4 LM-sampler and LMM-sampler |
| LM-sampler | 9.1 Introduction to lm_auto and lm_pval |
| lm_auto introduction | 9.1 Introduction to lm_auto and lm_pval |
| lm_auto sample output | 9.3 Running lm_auto example and sample output |
| lm_auto sample parameter file | 9.2 Sample lm_auto parameter file |
| lm_auto statements | 9.6 Autozyg statements |
| lm_bayes introduction | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| lm_bayes sample output | 11.5 Running lm_bayes examples and sample output |
| lm_bayes statements | 11.7 Location LOD scores statements |
| lm_ibdtests introduction | 10.1 Introduction to lm_ibdtests |
| lm_ibdtests sample output | 10.3 Sample lm_ibdtests output |
| lm_ibdtests statements | 10.4 lm_ibdtests statements |
| lm_lods introduction | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| lm_lods sample output | 11.3 Running lm_lods example and sample output |
| lm_lods statements | 11.7 Location LOD scores statements |
| lm_map introduction | 13.1 Introduction to lm_map |
| lm_map sample output for genotypic data | 13.3 Running lm_map with genotypic data |
| lm_map sample output for phenotypic data | 13.4 Running lm_map with phenotypic data |
| lm_map statements | 13.5 lm_map statements |
| lm_markers introduction | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| lm_markers sample output | 11.4 Running lm_markers examples and sample output |
| lm_markers statements | 11.7 Location LOD scores statements |
| lm_multiple introduction | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| lm_pval introduction | 9.1 Introduction to lm_auto and lm_pval |
| lm_pval sample output | 9.5 Running lm_pval example and sample output |
| lm_pval sample parameter file | 9.4 Sample lm_pval parameter file |
| lm_pval statements | 9.6 Autozyg statements |
| lm_schnell introduction | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| lm_schnell sample output | 11.6 Running lm_schnell example and sample output |
| LMM-sampler | 8.4 LM-sampler and LMM-sampler |
| LMM-sampler | 8.4 LM-sampler and LMM-sampler |
| location LOD scores computational parameters | 11.7.7 Location LOD scores computational parameters |
| location LOD scores computing requests | 11.7.1 Location LOD scores computing requests |
| location LOD scores estimates | 11. Estimating Location LOD Scores by MCMC |
| location LOD scores file identification statements | 11.7.2 Location LOD scores file identification statements |
| location LOD scores mapping model parameters | 11.7.5 Location LOD scores mapping model parameters |
| location LOD scores MCMC parameters and options | 11.7.8 Location LOD scores MCMC parameters and options |
| location LOD scores output file description | 11.7.4 Location LOD scores output file description |
| location LOD scores pedigree file description | 11.7.3 Location LOD scores pedigree file description |
| location LOD scores population model parameters | 11.7.6 Location LOD scores population model parameters |
| location LOD scores statements | 11.7 Location LOD scores statements |
| locus window | 9.6.7 Autozyg computational parameters |
| locus-by-locus sampling | 9.6.8 Autozyg MCMC parameters and options |
| locus-by-locus setup | 8.5 MCMC parameters and options |
|
| M | | |
|---|
| M-sampler | 8.4 LM-sampler and LMM-sampler |
| M-sampler | 9.2 Sample lm_auto parameter file |
| M-sampler | 9.6.8 Autozyg MCMC parameters and options |
| M-sampler | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| major gene model | 5.1 Introduction to genedrop. |
| marker allele frequencies | 6.5.3 markerdrop population model parameters |
| marker data | 9.6.7 Autozyg computational parameters |
| marker data file | 2.3 File identification statements |
| marker data file | 9.2 Sample lm_auto parameter file |
| marker names | 6.5.3 markerdrop population model parameters |
| marker seeds | 6.5.4 markerdrop computational parameters |
| marker simulation using inheritance indicators | 6.5.1 markerdrop computing requests |
| marker simulation using trait | 6.5.1 markerdrop computing requests |
| markerdrop computational parameters | 6.5.4 markerdrop computational parameters |
| markerdrop computing requests | 6.5.1 markerdrop computing requests |
| markerdrop input file options | 6.5.5 markerdrop input file options |
| markerdrop introduction | 6.1 Introduction to markerdrop |
| markerdrop mapping model parameters | 6.5.2 markerdrop mapping model parameters |
| markerdrop output | 6.4 Running markerdrop examples and sample output |
| markerdrop parameter file -- conditional on inheritance pattern | 6.3 Sample markerdrop parameter file -- conditional on inheritance pattern |
| markerdrop parameter file -- conditional on trait | 6.2 Sample markerdrop parameter file -- conditional on trait |
| markerdrop population model parameters | 6.5.3 markerdrop population model parameters |
| markerdrop statements | 6.5 markerdrop statements |
| Markov chain Monte Carlo | 8. Using MCMC to Estimate Parameters of Interest in Pedigree Data |
| Markov chain Monte Carlo | 9.1 Introduction to lm_auto and lm_pval |
| Markov chain Monte Carlo | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| MC iterations | 8.5 MCMC parameters and options |
| MC iterations | 9.6.8 Autozyg MCMC parameters and options |
| MC iterations | 11.7.8 Location LOD scores MCMC parameters and options |
| MCMC introduction | 8. Using MCMC to Estimate Parameters of Interest in Pedigree Data |
| MCMC options | 8.5 MCMC parameters and options |
| MCMC parameters | 8.5 MCMC parameters and options |
| meiosis indicators | 5.4.5 genedrop output pedigree options |
| meiosis indicators | 6.1 Introduction to markerdrop |
| meiosis indicators | 7.1 Introduction to ibddrop |
| meiosis indicators | 7.4 ibddrop statements |
| meiosis indicators | 8.1 Specifying inheritance |
| meiosis indicators | 9.1 Introduction to lm_auto and lm_pval |
| meiosis indicators | 9.6.8 Autozyg MCMC parameters and options |
| meiosis indicators | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| meiosis indicators | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| missing marker data | 9.6.7 Autozyg computational parameters |
| missing quantitative trait data | 12.2 Sample multivar parameter file |
| mixed model | 5.1 Introduction to genedrop. |
| MORGAN | 1.1 Overview of MORGAN |
| MORGAN files | 2.1 Command syntax |
| MORGAN Gold standards | 1.5 Structure of the MORGAN package |
| MORGAN program libraries | 1.5 Structure of the MORGAN package |
| MORGAN subroutine libraries | 1.5 Structure of the MORGAN package |
| multivar | 12.1 Introduction to PolyEM programs |
| multivar computational options | 12.4.4 multivar computational options |
| multivar computational parameters | 12.4.3 multivar computational parameters |
| multivar computing requests | 12.4.1 multivar computing requests |
| multivar output options | 12.4.5 multivar output options |
| multivar sample output | 12.3 Running multivar example and sample output |
| multivar sample parameter file | 12.2 Sample multivar parameter file |
| multivar segregation model parameters | 12.4.2 multivar segregation model parameters |
| multivar statements | 12.4 multivar statements |
|