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Concept Index

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Index Entry Section

A
a priori ibd probabilities7. Estimating a priori ibd Probabilities by Monte Carlo
additive variance5.1 Introduction to genedrop.
additive variance5.2 Sample genedrop parameter file
additive variance5.4.3 genedrop population model parameters
affected individuals9.8.7 Autozyg computational parameters
allele frequencies5.4.3 genedrop population model parameters
allow statements2.4 Limit overriding
Autozyg computational parameters9.8.7 Autozyg computational parameters
Autozyg computing requests9.8.1 Autozyg computing requests
Autozyg file identification statements9.8.2 Autozyg file identification statements
Autozyg mapping model parameters9.8.5 Autozyg mapping model parameters
Autozyg MCMC parameters and options9.8.8 Autozyg MCMC parameters and options
Autozyg output file description9.8.4 Autozyg output file description
Autozyg pedigree file description9.8.3 Autozyg pedigree file description
Autozyg population model parameters9.8.6 Autozyg population model parameters
Autozyg programs9.1 Introduction to lm_auto, gl_auto and lm_pval
Autozyg statements9.8 Autozyg statements
autozygosity9.1 Introduction to lm_auto, gl_auto and lm_pval

B
bivar12.1 Introduction to PolyEM programs
block Gibbs sampler8.4 Single and multiple meiosis LM-samplers
burn-in8.5 MCMC computational options
burn-in8.6 MCMC parameter statements
burn-in8.6 MCMC parameter statements
burn-in9.2 Sample lm_auto parameter file

C
civil introduction10.1 Introduction to lm_ibdtests and civil
civil sample output10.5 Sample civil output
civil statements10.6 lm_ibdtests and civil statements
command line options2.1 Command syntax
command syntax2.1 Command syntax
component3.1 Introduction to pedcheck
component3.2 Sample pedcheck parameter file
component3.4 pedcheck statements
component4.4 kin statements
conditional ibd probabilities9. Estimating Conditional ibd Probabilities by MCMC
consistency (Mendelian) of marker data9.8.1 Autozyg computing requests
continuous trait specification for lod score calculation11.2 Sample parameter files for lm_linkage and lm_bayes

D
debug control2.5 Output control
descent graph9.1 Introduction to lm_auto, gl_auto and lm_pval
discrete trait6.5.4 markerdrop computational parameters
discrete trait9.8.7 Autozyg computational parameters
discrete trait specification for lod score calculation11.2 Sample parameter files for lm_linkage and lm_bayes
display options2.5 Output control

E
EM algorithm12. Polygenic Modeling of Quantitative Traits by EM Algorithm
exact computation9.4 Sample gl_auto parameter file
exact computations8.3 Exact HMM computations
extra file2.3 File identification statements

F
file names2.3 File identification statements
file separator2.6 Pedigree file
file type codes2.1 Command syntax
founder gene labels5.1 Introduction to genedrop.
founder gene labels5.2 Sample genedrop parameter file
founder gene labels5.4.5 genedrop output pedigree options
founder gene labels6.4 Running markerdrop examples and sample output
founder gene labels8.1 Specifying inheritance
founder genome labels5.1 Introduction to genedrop.
founder genome labels8.1 Specifying inheritance
founder genome labels9.4 Sample gl_auto parameter file
founder genome labels9.8.4 Autozyg output file description
fuzzy p-value9.7 Running lm_pval example and sample output

G
gender2.7 Pedigree file description statements
gender3.4 pedcheck statements
gender--specific maps5.4.2 genedrop mapping model parameters
gender--specific maps9.2 Sample lm_auto parameter file
gender--specific maps11.2 Sample parameter files for lm_linkage and lm_bayes
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 output5.3 Running genedrop examples and sample output
genedrop sample parameter file5.2 Sample genedrop parameter file
genedrop statements5.4 genedrop statements
genetic map estimation13. Estimating Genetic Maps from Marker Data
genetic model8.2 Genetic model
genotypic trait9.2 Sample lm_auto parameter file
genotypic trait9.8.7 Autozyg computational parameters
genotypic trait specification for lod score calculation11.2 Sample parameter files for lm_linkage and lm_bayes
gl_auto introduction9.1 Introduction to lm_auto, gl_auto and lm_pval
gl_auto sample output9.5 Running gl_auto example and sample output
gl_auto sample parameter file9.4 Sample gl_auto parameter file
gl_auto statements9.8 Autozyg statements
GLUT runtime display2.5 Output control

H
Haldane map function5.4.2 genedrop mapping model parameters
Haldane map function6.5.2 markerdrop mapping model parameters
Haldane map function6.5.2 markerdrop mapping model parameters
Haldane map function7.2 Sample ibddrop parameter file
Haldane map function11.8.5 Location lod scores mapping model parameters
HMM computations8.3 Exact HMM computations
how to get the examples1.3 Get and set up the examples
how to get the tutorial1.2 Get the Tutorial

I
ibd4.1 Introduction to kin
ibd7. Estimating a priori ibd Probabilities by Monte Carlo
ibd8.1 Specifying inheritance
ibd9. Estimating Conditional ibd Probabilities by MCMC
ibd graph9.1 Introduction to lm_auto, gl_auto and lm_pval
ibd graph9.4 Sample gl_auto parameter file
ibd measures10.6 lm_ibdtests and civil statements
ibd pattern7.1 Introduction to ibddrop
ibd pattern7.3 Running ibddrop example and sample output
ibd pattern9.3 Running lm_auto example and sample output
ibd-based tests10. Estimating ibd Based Test Statistics by MCMC
ibddrop introduction7.1 Introduction to ibddrop
ibddrop sample output7.3 Running ibddrop example and sample output
ibddrop sample parameter file7.2 Sample ibddrop parameter file
ibddrop statements7.4 ibddrop statements
identity by descent7. Estimating a priori ibd Probabilities by Monte Carlo
identity by descent9. Estimating Conditional ibd Probabilities by MCMC
identity by descent9.1 Introduction to lm_auto, gl_auto and lm_pval
inbreeding coefficient4.1 Introduction to kin
inbreeding coefficient4.4 kin statements
incomplete penetrance6.5.4 markerdrop computational parameters
incomplete penetrance9.8.7 Autozyg computational parameters
incomplete penetrances6.1 Introduction to markerdrop
inheritance indicators5.4.5 genedrop output pedigree options
inheritance indicators6.1 Introduction to markerdrop
inheritance indicators7.1 Introduction to ibddrop
inheritance indicators7.4 ibddrop statements
inheritance indicators8.1 Specifying inheritance
inheritance indicators8.6 MCMC parameter statements
inheritance indicators9.1 Introduction to lm_auto, gl_auto and lm_pval
inheritance vector8.1 Specifying inheritance

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