| 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 –See also map function | 5.4.2 genedrop mapping model parameters |
|
| L | | |
|---|
| L-sampler | 8.4 Single and multiple meiosis LM-samplers |
| L-sampler | 8.6 MCMC parameter statements |
| L-sampler | 9.2 Sample lm_auto parameter file |
| L-sampler | 11.2 Sample parameter files for lm_linkage and lm_bayes |
| L-sampler probability | 8.4 Single and multiple meiosis LM-samplers |
| latent p-values | 9.1 Introduction to lm_auto, gl_auto and lm_pval |
| latent p-values | 10.4 Sample civil parameter file |
| liability class specification | 11.2 Sample parameter files for lm_linkage and lm_bayes |
| liability classes | 9.8.7 Autozyg computational parameters |
| likelihood-ratio measures | 10.6 lm_ibdtests and civil statements |
| limit overriding | 2.4 Limit overriding |
| limit statements | 2.4 Limit overriding |
| line length limit | 2.2 Parameter file |
| LINKAGE package format | 4.5 The translink utility |
| LM-sampler | 8.4 Single and multiple meiosis LM-samplers |
| LM-sampler | 9.1 Introduction to lm_auto, gl_auto and lm_pval |
| lm_auto introduction | 9.1 Introduction to lm_auto, gl_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 | 9.8 Autozyg statements |
| lm_bayes introduction | 11.1 Introduction to lm_linkage, lm_bayes, lm_twoqtl, gl_lods and base_trait_lods |
| lm_bayes sample output | 11.4 Running lm_bayes examples and sample output |
| lm_bayes statements | 11.9 Location lod scores statements |
| lm_ibdtests introduction | 10.1 Introduction to lm_ibdtests and civil |
| lm_ibdtests sample output | 10.3 Sample lm_ibdtests output |
| lm_ibdtests statements | 10.6 lm_ibdtests and civil statements |
| lm_linkage introduction | 11.1 Introduction to lm_linkage, lm_bayes, lm_twoqtl, gl_lods and base_trait_lods |
| lm_linkage sample output | 11.3 Running lm_linkage examples and sample output |
| lm_linkage statements | 11.9 Location lod scores statements |
| lm_map introduction | 14.1 Introduction to lm_map |
| lm_map sample output for genotypic data | 14.3 Running lm_map with genotypic data |
| lm_map sample output for phenotypic data | 14.4 Running lm_map with phenotypic data |
| lm_map statements | 14.5 lm_map statements |
| lm_pval introduction | 9.1 Introduction to lm_auto, gl_auto and lm_pval |
| lm_pval sample output | 9.7 Running lm_pval example and sample output |
| lm_pval sample parameter file | 9.6 Sample lm_pval parameter file |
| lm_pval statements | 9.8 Autozyg statements |
| lm_twoqtl introduction | 11.1 Introduction to lm_linkage, lm_bayes, lm_twoqtl, gl_lods and base_trait_lods |
| lm_twoqtl sample output | 11.5 Running lm_twoqtl examples and sample output |
| location lod scores computational parameters | 11.9.7 Location lod scores computational parameters |
| location lod scores computing requests | 11.9.1 Location lod scores computing requests |
| location lod scores estimates | 11. Estimating Location lod Scores by MCMC |
| location lod scores file identification statements | 11.9.2 Location lod scores file identification statements |
| location lod scores mapping model parameters | 11.9.5 Location lod scores mapping model parameters |
| location lod scores MCMC parameters and options | 11.9.8 Location lod scores MCMC parameters and options |
| location lod scores output file description | 11.9.4 Location lod scores output file description |
| location lod scores pedigree file description | 11.9.3 Location lod scores pedigree file description |
| location lod scores population model parameters | 11.9.6 Location lod scores population model parameters |
| location lod scores statements | 11.9 Location lod scores statements |
| locus window | 9.8.7 Autozyg computational parameters |
| locus-by-locus sampling | 8.6 MCMC parameter statements |
| locus-by-locus setup | 8.5 MCMC computational options |
|
| M | | |
|---|
| M-sampler | 8.4 Single and multiple meiosis LM-samplers |
| M-sampler | 8.6 MCMC parameter statements |
| M-sampler | 9.2 Sample lm_auto parameter file |
| M-sampler | 11.2 Sample parameter files for lm_linkage and lm_bayes |
| major gene model | 5.1 Introduction to genedrop. |
| map function | 5.4.2 genedrop mapping model parameters |
| map function | 6.5.2 markerdrop mapping model parameters |
| map function | 6.5.2 markerdrop mapping model parameters |
| map function | 7.2.1 Classic ibddrop parameter file |
| map function | 11.9.5 Location lod scores mapping model parameters |
| map test tlocs jointly at markers | 11.5 Running lm_twoqtl examples and sample output |
| marker allele frequencies | 6.5.3 markerdrop population model parameters |
| marker data | 9.8.7 Autozyg computational parameters |
| marker data | 12.1 Introduction to ibd_create and ibd_haplo |
| 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 | 6.5.1 markerdrop computing requests |
| marker simulation using meiosis 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, gl_auto and lm_pval |
| Markov chain Monte Carlo | 11.1 Introduction to lm_linkage, lm_bayes, lm_twoqtl, gl_lods and base_trait_lods |
| MC iterations | 8.5 MCMC computational options |
| MC iterations | 8.6 MCMC parameter statements |
| MC iterations | 11.9.8 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 computational options |
| MCMC parameter statements | 8.6 MCMC parameter statements |
| 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 | 8.6 MCMC parameter statements |
| meiosis indicators | 9.1 Introduction to lm_auto, gl_auto and lm_pval |
| meiosis indicators | 11.1 Introduction to lm_linkage, lm_bayes, lm_twoqtl, gl_lods and base_trait_lods |
| meiosis indicators | 11.2 Sample parameter files for lm_linkage and lm_bayes |
| missing marker data | 9.8.7 Autozyg computational parameters |
| missing quantitative trait data | 13.2 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 package structure | 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 |
| multiple meiosis sampler | 8.4 Single and multiple meiosis LM-samplers |
| multiple meiosis sampler | 8.4 Single and multiple meiosis LM-samplers |
| multiple meiosis sampler | 9.1 Introduction to lm_auto, gl_auto and lm_pval |
| multiple meiosis sampler | 9.4 Sample gl_auto parameter file |
| multiple meiosis sampler | 11.1 Introduction to lm_linkage, lm_bayes, lm_twoqtl, gl_lods and base_trait_lods |
| multiple meiosis sampler | 11.2 Sample parameter files for lm_linkage and lm_bayes |
| multivar | 13.1 Introduction to PolyEM programs |
| multivar computational options | 13.4.4 multivar computational options |
| multivar computational parameters | 13.4.3 multivar computational parameters |
| multivar computing requests | 13.4.1 multivar computing requests |
| multivar output options | 13.4.5 multivar output options |
| multivar sample output | 13.3 Running multivar example and sample output |
| multivar sample parameter file | 13.2 Sample multivar parameter file |
| multivar segregation model parameters | 13.4.2 multivar segregation model parameters |
| multivar statements | 13.4 multivar statements |
|