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Concept Index
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A
B
C
E
F
G
H
I
K
L
M
N
O
P
Q
S
T
U
Index Entry
Section
A
a priori
ibd
probabilities
6. Estimating
a priori
ibd
Probabilities by Monte Carlo
affected individuals
7.6.4 Autozyg computational parameters
allele frequencies
5.4.3
genedrop
population model parameters
Autozyg computational parameters
7.6.4 Autozyg computational parameters
Autozyg computing requests
7.6.1 Autozyg computing requests
Autozyg mapping model parameters
7.6.2 Autozyg mapping model parameters
Autozyg MCMC parameters and options
7.6.5 Autozyg MCMC parameters and options
Autozyg population model parameters
7.6.3 Autozyg population model parameters
Autozyg programs
7.1 Introduction to
lm_auto
and
lm_pval
Autozyg statements
7.6 Autozyg statements
autozygosity
7.1 Introduction to
lm_auto
and
lm_pval
B
bivar
9.1 Introduction to PolyEM programs
burn-in
7.2 Sample
lm_auto
parameter file
burn-in
7.6.5 Autozyg MCMC parameters and options
burn-in
8.8.5 Location LOD scores MCMC parameters and options
C
command line options
2.1 Command syntax
command syntax
2.1 Command syntax
Comparison of location LOD scores methods
8.7 Comparison of LOD scores methods
E
eigenvalue method
8.1 Introduction to
lm_lods
,
lm_markers
and
lm_bayes
eigenvalue method
8.3 Sample
lm_lods
output
EM algorithm
9. Polygenic Modeling of Quantitative Traits by EM Algorithm
F
file names
2.3 File identification statements
file separator
2.4 Pedigree file
file type codes
2.1 Command syntax
founder labels
5.1 Introduction to
genedrop
.
founder labels
5.4.5
genedrop
output pedigree options
G
gender
2.5 Pedigree file description statements
gender--specific maps
5.4.2
genedrop
mapping model parameters
gender--specific maps
7.2 Sample
lm_auto
parameter file
gender--specific maps
8.2 Sample
lm_lods
parameter file
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 file
5.3 Sample
genedrop
output file
genedrop
sample parameter file
5.2 Sample
genedrop
parameter file
genedrop
statements
5.4
genedrop
statements
H
Haldane map function
5.4.2
genedrop
mapping model parameters
Haldane map function
6.2 Sample
ibddrop
parameter file
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
6. Estimating
a priori
ibd
Probabilities by Monte Carlo
ibd
7. Estimating Posterior
ibd
Probabilities by MCMC
ibddrop
introduction
6.1 Introduction to
ibddrop
ibddrop
sample output
6.3 Sample
ibddrop
output
ibddrop
sample parameter file
6.2 Sample
ibddrop
parameter file
ibddrop
statements
6.4
ibddrop
statements
identity by descent
6. Estimating
a priori
ibd
Probabilities by Monte Carlo
identity by descent
7. Estimating Posterior
ibd
Probabilities by MCMC
inbreeding coefficients
4.1 Introduction to
kin
K
kin
introduction
4.1 Introduction to
kin
kin
sample output
4.3 Sample
kin
output
kin
sample parameter file
4.2 Sample
kin
parameter file
kin
statements
4.4
kin
statements
kinship coefficients
4.1 Introduction to
kin
L
L-sampler
7.2 Sample
lm_auto
parameter file
L-sampler
7.6.5 Autozyg MCMC parameters and options
L-sampler
8.2 Sample
lm_lods
parameter file
LM-sampler
7.1 Introduction to
lm_auto
and
lm_pval
lm_auto
introduction
7.1 Introduction to
lm_auto
and
lm_pval
lm_auto
sample output
7.3 Sample
lm_auto
output
lm_auto
sample parameter file
7.2 Sample
lm_auto
parameter file
lm_auto
statements
7.6 Autozyg statements
lm_bayes
introduction
8.1 Introduction to
lm_lods
,
lm_markers
and
lm_bayes
lm_bayes
sample output
8.6 Sample
lm_bayes
output
lm_bayes
sample parameter file
8.5 Sample
lm_bayes
parameter file
lm_bayes
statements
8.8 Location LOD scores statements
lm_lods
introduction
8.1 Introduction to
lm_lods
,
lm_markers
and
lm_bayes
lm_lods
sample output
8.3 Sample
lm_lods
output
lm_lods
sample parameter file
8.2 Sample
lm_lods
parameter file
lm_lods
statements
8.8 Location LOD scores statements
lm_markers
introduction
8.1 Introduction to
lm_lods
,
lm_markers
and
lm_bayes
lm_markers
sample output
8.4 Sample
lm_markers
output
lm_markers
statements
8.8 Location LOD scores statements
lm_pval
introduction
7.1 Introduction to
lm_auto
and
lm_pval
lm_pval
sample output
7.5 Sample
lm_pval
output
lm_pval
sample parameter file
7.4 Sample
lm_pval
parameter file
lm_pval
statements
7.6 Autozyg statements
location LOD scores computational parameters
8.8.4 Location LOD scores computational parameters
location LOD scores computing requests
8.8.1 Location LOD scores computing requests
location LOD scores estimates
8. Estimating Location LOD Scores by MCMC
location LOD scores mapping model parameters
8.8.2 Location LOD scores mapping model parameters
location LOD scores MCMC parameters and options
8.8.5 Location LOD scores MCMC parameters and options
location LOD scores population model parameters
8.8.3 Location LOD scores population model parameters
location LOD scores statements
8.8 Location LOD scores statements
M
M-sampler
7.2 Sample
lm_auto
parameter file
M-sampler
7.6.5 Autozyg MCMC parameters and options
M-sampler
8.2 Sample
lm_lods
parameter file
marker data
7.6.4 Autozyg computational parameters
marker data file
2.3 File identification statements
Markov chain Monte Carlo
7.1 Introduction to
lm_auto
and
lm_pval
Markov chain Monte Carlo
8.1 Introduction to
lm_lods
,
lm_markers
and
lm_bayes
meiosis indicators
5.4.5
genedrop
output pedigree options
meiosis indicators
6.4
ibddrop
statements
meiosis indicators
7.1 Introduction to
lm_auto
and
lm_pval
meiosis indicators
7.6.5 Autozyg MCMC parameters and options
meiosis indicators
8.1 Introduction to
lm_lods
,
lm_markers
and
lm_bayes
meiosis indicators
8.2 Sample
lm_lods
parameter file
missing marker data
7.6.4 Autozyg computational parameters
missing quantitative trait data
9.2 Sample
multivar
parameter file
MORGAN
1.1 Overview of
MORGAN
MORGAN
files
2.1 Command syntax
multivar
9.1 Introduction to PolyEM programs
multivar
computational options
9.4.4
multivar
computational options
multivar
computational parameters
9.4.3
multivar
computational parameters
multivar
computing requests
9.4.1
multivar
computing requests
multivar
output options
9.4.5
multivar
output options
multivar
sample output
9.3 Sample
multivar
output
multivar
sample parameter file
9.2 Sample
multivar
parameter file
multivar
segregation model parameters
9.4.2
multivar
segregation model parameters
multivar
statements
9.4
multivar
statements
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A
B
C
E
F
G
H
I
K
L
M
N
O
P
Q
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T
U
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