| Index Entry | Section |
|---|
|
| N | | |
|---|
| names of individuals | 2.4 Pedigree file |
| non-genetic model | 5.1 Introduction to genedrop. |
|
| O | | |
|---|
| observed individuals | 2.4 Pedigree file |
| observed individuals | 12.4.3 multivar computational parameters |
| overview of MORGAN | 1.1 Overview of MORGAN |
|
| P | | |
|---|
| parameter file | 2.2 Parameter file |
| parameter statements | 2.2 Parameter file |
| parameter statements in pedigree files | 2.4 Pedigree file |
| pedcheck examples | 3.3 Running pedcheck examples |
| pedcheck introduction | 3.1 Introduction to pedcheck |
| pedcheck sample parameter file | 3.2 Sample pedcheck parameter file |
| pedcheck statements | 3.4 pedcheck statements |
| pedigree component | 3.2 Sample pedcheck parameter file |
| pedigree component | 3.4 pedcheck statements |
| pedigree component | 4.4 kin statements |
| pedigree file | 2.3 File identification statements |
| pedigree file | 2.4 Pedigree file |
| pedigree file descriptions | 2.5 Pedigree file description statements |
| pedigree options | 3.4 pedcheck statements |
| pedigree order | 3.4 pedcheck statements |
| pedigree peeling | 8.4 LM-sampler and LMM-sampler |
| pedigree record format | 2.5 Pedigree file description statements |
| pedigree record format | 6.5.5 markerdrop input file options |
| pedigree size | 2.5 Pedigree file description statements |
| pedigree trait data order | 2.5 Pedigree file description statements |
| pedigree validity | 3.1 Introduction to pedcheck |
| penetrance | 6.5.4 markerdrop computational parameters |
| penetrance | 8.2 Genetic model |
| phenotypic trait specification for lod score calculation | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| PolyEM | 12. Polygenic Modeling of Quantitative Traits by EM Algorithm |
| PolyEM introduction | 12.1 Introduction to PolyEM programs |
| PolyEM statements | 12.4 multivar statements |
| polygenic model | 5.1 Introduction to genedrop. |
| polygenic model | 12. Polygenic Modeling of Quantitative Traits by EM Algorithm |
| proband gametes | 7.2 Sample ibddrop parameter file |
| proband gametes | 7.4 ibddrop statements |
| proband gametes | 9.2 Sample lm_auto parameter file |
| proband gametes | 9.3 Running lm_auto example and sample output |
| proband gametes | 9.6.7 Autozyg computational parameters |
| pseudo-prior | 11.7.7 Location LOD scores computational parameters |
| pseudo-prior iterations | 8.5 MCMC parameters and options |
|
| Q | | |
|---|
| quantitative trait | 5.1 Introduction to genedrop. |
| quantitative trait | 9.6.7 Autozyg computational parameters |
| quantitative trait | 11.7.3 Location LOD scores pedigree file description |
| quantitative trait | 12. Polygenic Modeling of Quantitative Traits by EM Algorithm |
| quantitative trait specification for lod score calculation | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
|
| R | | |
|---|
| Rao-Blackwellized estimates | 11.5 Running lm_bayes examples and sample output |
| Rao-Blackwellized estimates | 11.7.2 Location LOD scores file identification statements |
| README documentation files | 1.5 Structure of the MORGAN package |
| recombination | 4.4 kin statements |
| rescue file | 9.6.2 Autozyg file identification statements |
| residual variance | 5.2 Sample genedrop parameter file |
| residual variance | 5.4.3 genedrop population model parameters |
| running genedrop examples | 5.3 Running genedrop examples and sample output |
| running ibddrop example | 7.3 Running ibddrop example and sample output |
| running kin example | 4.3 Running kin example and sample output |
| running lm_auto example | 9.3 Running lm_auto example and sample output |
| running lm_bayes examples | 11.5 Running lm_bayes examples and sample output |
| running lm_lods example | 11.3 Running lm_lods example and sample output |
| running lm_map with genotypic data | 13.3 Running lm_map with genotypic data |
| running lm_map with phenotypic data | 13.4 Running lm_map with phenotypic data |
| running lm_markers examples | 11.4 Running lm_markers examples and sample output |
| running lm_pval example | 9.5 Running lm_pval example and sample output |
| running lm_schnell example | 11.6 Running lm_schnell example and sample output |
| running markderdrop examples | 6.4 Running markerdrop examples and sample output |
| running multivar example | 12.3 Running multivar example and sample output |
|
| S | | |
|---|
| sample by scan | 8.5 MCMC parameters and options |
| sample by scan | 9.6.8 Autozyg MCMC parameters and options |
| sample by step | 8.5 MCMC parameters and options |
| sample by step | 9.6.8 Autozyg MCMC parameters and options |
| sample parameter file for lm_bayes | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| sample parameter file for lm_ibdtests | 10.2 Sample lm_ibdtests parameter file |
| sample parameter file for lm_lods | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| sample parameter file for lm_map | 13.2 Sample lm_map parameter file |
| sample parameter file for lm_markers | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| sample parameter file for lm_schnell | 11.2 Sample parameter files for lm_lods, lm_markers, lm_bayes and lm_schnell |
| schnell | 11.1 Introduction to lm_lods, lm_markers and lm_multiple, lm_bayes and lm_schnell |
| scores file | 9.6.2 Autozyg file identification statements |
| scoreset | 9.6.7 Autozyg computational parameters |
| scoreset | 9.6.7 Autozyg computational parameters |
| seed file | 2.3 File identification statements |
| seed file | 5.2 Sample genedrop parameter file |
| seed file | 7.2 Sample ibddrop parameter file |
| seed file | 9.6.2 Autozyg file identification statements |
| seeds for data simulation | 5.1 Introduction to genedrop. |
| seeds for data simulation | 5.3 Running genedrop examples and sample output |
| seeds for data simulation | 5.4.4 genedrop computational parameters |
| seeds for data simulation | 5.4.6 genedrop output seed file options |
| seeds for sampler | 7.2 Sample ibddrop parameter file |
| seeds for sampler | 7.4 ibddrop statements |
| sequential imputation | 8.5 MCMC parameters and options |
| sequential imputation | 9.6.8 Autozyg MCMC parameters and options |
| sequential imputation proposals | 11.7.8 Location LOD scores MCMC parameters and options |
| simulating marker data | 5. Simulating Marker and Trait Data in Pedigrees |
| simulating marker data | 5.4.4 genedrop computational parameters |
| simulating trait data | 5. Simulating Marker and Trait Data in Pedigrees |
| simulating trait data | 5.4.4 genedrop computational parameters |
| structure of the MORGAN package | 1.5 Structure of the MORGAN package |
|
| T | | |
|---|
| trait data | 6.5.4 markerdrop computational parameters |
| trait data | 9.2 Sample lm_auto parameter file |
| trait data | 9.6.7 Autozyg computational parameters |
| trait frequencies | 6.5.3 markerdrop population model parameters |
| trait model | 6.1 Introduction to markerdrop |
| trait seeds | 6.5.4 markerdrop computational parameters |
| trait test positions | 11.7.5 Location LOD scores mapping model parameters |
| Tutorial for LOD score examples with `ped73.ped' | 1.4 Overview of the pedigrees used in the examples |
|