| Index Entry | Section |
|---|
|
| A | | |
|---|
| a priori ibd probabilities | 7. Estimating a priori ibd Probabilities by Monte Carlo |
| additive variance | 5.1 Introduction to genedrop. |
| additive variance | 5.2 Sample genedrop parameter file |
| additive variance | 5.4.3 genedrop population model parameters |
| affected individuals | 9.6.7 Autozyg computational parameters |
| allele frequencies | 5.4.3 genedrop population model parameters |
| Autozyg computational parameters | 9.6.7 Autozyg computational parameters |
| Autozyg computing requests | 9.6.1 Autozyg computing requests |
| Autozyg file identification statements | 9.6.2 Autozyg file identification statements |
| Autozyg mapping model parameters | 9.6.5 Autozyg mapping model parameters |
| Autozyg MCMC parameters and options | 9.6.8 Autozyg MCMC parameters and options |
| Autozyg output file description | 9.6.4 Autozyg output file description |
| Autozyg pedigree file description | 9.6.3 Autozyg pedigree file description |
| Autozyg population model parameters | 9.6.6 Autozyg population model parameters |
| Autozyg programs | 9.1 Introduction to lm_auto and lm_pval |
| Autozyg statements | 9.6 Autozyg statements |
| autozygosity | 9.1 Introduction to lm_auto and lm_pval |
|
| B | | |
|---|
| bivar | 12.1 Introduction to PolyEM programs |
| block Gibbs sampler | 8.4 LM-sampler and LMM-sampler |
| burn-in | 8.5 MCMC parameters and options |
| burn-in | 9.2 Sample lm_auto parameter file |
| burn-in | 9.6.8 Autozyg MCMC parameters and options |
| burn-in | 9.6.8 Autozyg MCMC parameters and options |
| burn-in | 11.7.8 Location LOD scores MCMC parameters and options |
|
| C | | |
|---|
| command line options | 2.1 Command syntax |
| command syntax | 2.1 Command syntax |
| component | 3.1 Introduction to pedcheck |
| component | 3.2 Sample pedcheck parameter file |
| component | 3.4 pedcheck statements |
| component | 4.4 kin statements |
| conditional ibd probabilities | 9. Estimating Conditional ibd Probabilities by MCMC |
| continuous trait specification for lod score calculation | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
|
| D | | |
|---|
| discrete trait | 6.5.4 markerdrop computational parameters |
| discrete trait | 9.6.7 Autozyg computational parameters |
| discrete trait specification for lod score calculation | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
|
| E | | |
|---|
| eigenvalue method | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| eigenvalue method | 11.3 Running lm_lods example and sample output |
| EM algorithm | 12. Polygenic Modeling of Quantitative Traits by EM Algorithm |
| exact computations | 8.3 Exact HMM computations |
|
| F | | |
|---|
| file names | 2.3 File identification statements |
| file separator | 2.4 Pedigree file |
| file type codes | 2.1 Command syntax |
| founder gene labels | 5.1 Introduction to genedrop. |
| founder gene labels | 5.2 Sample genedrop parameter file |
| founder gene labels | 5.4.5 genedrop output pedigree options |
| founder gene labels | 6.4 Running markerdrop examples and sample output |
| founder gene labels | 8.1 Specifying inheritance |
| fuzzy p-value | 9.5 Running lm_pval example and sample output |
|
| G | | |
|---|
| gender | 2.5 Pedigree file description statements |
| gender | 3.4 pedcheck statements |
| gender--specific maps | 5.4.2 genedrop mapping model parameters |
| gender--specific maps | 9.2 Sample lm_auto parameter file |
| gender--specific maps | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| genedrop computational parameters | 5.4.4 genedrop computational parameters |
| genedrop computing requests | 5.4.1 genedrop computing requests |
| genedrop introduction | 5.1 Introduction to genedrop. |
| genedrop mapping model parameters | 5.4.2 genedrop mapping model parameters |
| genedrop output pedigree options | 5.4.5 genedrop output pedigree options |
| genedrop output seed file | 5.4.6 genedrop output seed file options |
| genedrop population model parameters | 5.4.3 genedrop population model parameters |
| genedrop sample output | 5.3 Running genedrop examples and sample output |
| genedrop sample parameter file | 5.2 Sample genedrop parameter file |
| genedrop statements | 5.4 genedrop statements |
| genetic map estimation | 13. Estimating Genetic Map from Marker Data |
| genetic model | 8.2 Genetic model |
| genotypic trait | 9.2 Sample lm_auto parameter file |
| genotypic trait | 9.6.7 Autozyg computational parameters |
| genotypic trait specification for lod score calculation | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
|
| H | | |
|---|
| Haldane map function | 5.4.2 genedrop mapping model parameters |
| Haldane map function | 6.5.2 markerdrop mapping model parameters |
| Haldane map function | 6.5.2 markerdrop mapping model parameters |
| Haldane map function | 7.2 Sample ibddrop parameter file |
| Haldane map function | 11.7.5 Location LOD scores mapping model parameters |
| HMM computations | 8.3 Exact HMM computations |
| how to get the examples | 1.3 Get and set up the examples |
| how to get the tutorial | 1.2 Get the Tutorial |
|
| I | | |
|---|
| ibd | 4.1 Introduction to kin |
| ibd | 7. Estimating a priori ibd Probabilities by Monte Carlo |
| ibd | 8.1 Specifying inheritance |
| ibd | 9. Estimating Conditional ibd Probabilities by MCMC |
| ibd | 9.1 Introduction to lm_auto and lm_pval |
| ibd measures | 10.4 lm_ibdtests statements |
| ibd pattern | 7.1 Introduction to ibddrop |
| ibd pattern | 7.3 Running ibddrop example and sample output |
| ibd pattern | 9.3 Running lm_auto example and sample output |
| ibd-based tests | 10. Estimating ibd Based Test Statistics by MCMC |
| ibddrop introduction | 7.1 Introduction to ibddrop |
| ibddrop sample output | 7.3 Running ibddrop example and sample output |
| ibddrop sample parameter file | 7.2 Sample ibddrop parameter file |
| ibddrop statements | 7.4 ibddrop statements |
| identity by descent | 7. Estimating a priori ibd Probabilities by Monte Carlo |
| identity by descent | 9. Estimating Conditional ibd Probabilities by MCMC |
| identity by descent | 9.1 Introduction to lm_auto and lm_pval |
| inbreeding coefficient | 4.1 Introduction to kin |
| inbreeding coefficient | 4.4 kin statements |
| incomplete penetrance | 6.1 Introduction to markerdrop |
| incomplete penetrance | 6.5.4 markerdrop computational parameters |
| incomplete penetrance | 9.6.7 Autozyg computational parameters |
| inheritance indicators | 5.4.5 genedrop output pedigree options |
| inheritance indicators | 6.1 Introduction to markerdrop |
| inheritance indicators | 7.1 Introduction to ibddrop |
| inheritance indicators | 7.4 ibddrop statements |
| inheritance indicators | 8.1 Specifying inheritance |
| inheritance indicators | 9.1 Introduction to lm_auto and lm_pval |
| inheritance indicators | 9.6.8 Autozyg MCMC parameters and options |
| inheritance vector | 8.1 Specifying inheritance |
|