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Concept Index

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Index Entry Section

A
a priori ibd probabilities6. Estimating a priori ibd Probabilities by Monte Carlo
affected individuals7.6.4 Autozyg computational parameters
allele frequencies5.4.3 genedrop population model parameters
Autozyg computational parameters7.6.4 Autozyg computational parameters
Autozyg computing requests7.6.1 Autozyg computing requests
Autozyg mapping model parameters7.6.2 Autozyg mapping model parameters
Autozyg MCMC parameters and options7.6.5 Autozyg MCMC parameters and options
Autozyg population model parameters7.6.3 Autozyg population model parameters
Autozyg programs7.1 Introduction to lm_auto and lm_pval
Autozyg statements7.6 Autozyg statements
autozygosity7.1 Introduction to lm_auto and lm_pval

B
bivar9.1 Introduction to PolyEM programs
burn-in7.2 Sample lm_auto parameter file
burn-in7.6.5 Autozyg MCMC parameters and options
burn-in8.8.5 Location LOD scores MCMC parameters and options

C
command line options2.1 Command syntax
command syntax2.1 Command syntax
Comparison of location LOD scores methods8.7 Comparison of LOD scores methods

E
eigenvalue method8.1 Introduction to lm_lods, lm_markers and lm_bayes
eigenvalue method8.3 Sample lm_lods output
EM algorithm9. Polygenic Modeling of Quantitative Traits by EM Algorithm

F
file names2.3 File identification statements
file separator2.4 Pedigree file
file type codes2.1 Command syntax
founder labels5.1 Introduction to genedrop.
founder labels5.4.5 genedrop output pedigree options

G
gender2.5 Pedigree file description statements
gender--specific maps5.4.2 genedrop mapping model parameters
gender--specific maps7.2 Sample lm_auto parameter file
gender--specific maps8.2 Sample lm_lods parameter file
genedrop computational parameters5.4.4 genedrop computational parameters
genedrop computing requests5.4.1 genedrop computing requests
genedrop introduction5.1 Introduction to genedrop.
genedrop mapping model parameters5.4.2 genedrop mapping model parameters
genedrop output pedigree options5.4.5 genedrop output pedigree options
genedrop output seed file5.4.6 genedrop output seed file options
genedrop population model parameters5.4.3 genedrop population model parameters
genedrop sample output file5.3 Sample genedrop output file
genedrop sample parameter file5.2 Sample genedrop parameter file
genedrop statements5.4 genedrop statements

H
Haldane map function5.4.2 genedrop mapping model parameters
Haldane map function6.2 Sample ibddrop parameter file
how to get the examples1.3 Get and set up the examples
how to get the tutorial1.2 Get the Tutorial

I
ibd6. Estimating a priori ibd Probabilities by Monte Carlo
ibd7. Estimating Posterior ibd Probabilities by MCMC
ibddrop introduction6.1 Introduction to ibddrop
ibddrop sample output6.3 Sample ibddrop output
ibddrop sample parameter file6.2 Sample ibddrop parameter file
ibddrop statements6.4 ibddrop statements
identity by descent6. Estimating a priori ibd Probabilities by Monte Carlo
identity by descent7. Estimating Posterior ibd Probabilities by MCMC
inbreeding coefficients4.1 Introduction to kin

K
kin introduction4.1 Introduction to kin
kin sample output4.3 Sample kin output
kin sample parameter file4.2 Sample kin parameter file
kin statements4.4 kin statements
kinship coefficients4.1 Introduction to kin

L
L-sampler7.2 Sample lm_auto parameter file
L-sampler7.6.5 Autozyg MCMC parameters and options
L-sampler8.2 Sample lm_lods parameter file
LM-sampler7.1 Introduction to lm_auto and lm_pval
lm_auto introduction7.1 Introduction to lm_auto and lm_pval
lm_auto sample output7.3 Sample lm_auto output
lm_auto sample parameter file7.2 Sample lm_auto parameter file
lm_auto statements7.6 Autozyg statements
lm_bayes introduction8.1 Introduction to lm_lods, lm_markers and lm_bayes
lm_bayes sample output8.6 Sample lm_bayes output
lm_bayes sample parameter file8.5 Sample lm_bayes parameter file
lm_bayes statements8.8 Location LOD scores statements
lm_lods introduction8.1 Introduction to lm_lods, lm_markers and lm_bayes
lm_lods sample output8.3 Sample lm_lods output
lm_lods sample parameter file8.2 Sample lm_lods parameter file
lm_lods statements8.8 Location LOD scores statements
lm_markers introduction8.1 Introduction to lm_lods, lm_markers and lm_bayes
lm_markers sample output8.4 Sample lm_markers output
lm_markers statements8.8 Location LOD scores statements
lm_pval introduction7.1 Introduction to lm_auto and lm_pval
lm_pval sample output7.5 Sample lm_pval output
lm_pval sample parameter file7.4 Sample lm_pval parameter file
lm_pval statements7.6 Autozyg statements
location LOD scores computational parameters8.8.4 Location LOD scores computational parameters
location LOD scores computing requests8.8.1 Location LOD scores computing requests
location LOD scores estimates8. Estimating Location LOD Scores by MCMC
location LOD scores mapping model parameters8.8.2 Location LOD scores mapping model parameters
location LOD scores MCMC parameters and options8.8.5 Location LOD scores MCMC parameters and options
location LOD scores population model parameters8.8.3 Location LOD scores population model parameters
location LOD scores statements8.8 Location LOD scores statements

M
M-sampler7.2 Sample lm_auto parameter file
M-sampler7.6.5 Autozyg MCMC parameters and options
M-sampler8.2 Sample lm_lods parameter file
marker data7.6.4 Autozyg computational parameters
marker data file2.3 File identification statements
Markov chain Monte Carlo7.1 Introduction to lm_auto and lm_pval
Markov chain Monte Carlo8.1 Introduction to lm_lods, lm_markers and lm_bayes
meiosis indicators5.4.5 genedrop output pedigree options
meiosis indicators6.4 ibddrop statements
meiosis indicators7.1 Introduction to lm_auto and lm_pval
meiosis indicators7.6.5 Autozyg MCMC parameters and options
meiosis indicators8.1 Introduction to lm_lods, lm_markers and lm_bayes
meiosis indicators8.2 Sample lm_lods parameter file
missing marker data7.6.4 Autozyg computational parameters
missing quantitative trait data9.2 Sample multivar parameter file
MORGAN1.1 Overview of MORGAN
MORGAN files2.1 Command syntax
multivar9.1 Introduction to PolyEM programs
multivar computational options9.4.4 multivar computational options
multivar computational parameters9.4.3 multivar computational parameters
multivar computing requests9.4.1 multivar computing requests
multivar output options9.4.5 multivar output options
multivar sample output9.3 Sample multivar output
multivar sample parameter file9.2 Sample multivar parameter file
multivar segregation model parameters9.4.2 multivar segregation model parameters
multivar statements9.4 multivar statements

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