Concept Index

Jump to:	A B C D E F G H I K L M N O P Q R S T U V W

	Index Entry	Section

A
	a priori ibd probabilities	7. Estimating a priori ibd Probabilities by Monte Carlo
	additive variance	5.1 Introduction to `genedrop`.
	additive variance	5.2 Sample `genedrop` parameter file
	additive variance	5.4.3 `genedrop` population model parameters
	affected individuals	9.8.7 Autozyg computational parameters
	age-of-onset penetrance specification	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	age-of-onset penetrances	9.8.7 Autozyg computational parameters
	allele frequencies	5.4.3 `genedrop` population model parameters
	allow statements	2.4 Limit overriding
	Autozyg computational parameters	9.8.7 Autozyg computational parameters
	Autozyg computing requests	9.8.1 Autozyg computing requests
	Autozyg file identification statements	9.8.2 Autozyg file identification statements
	Autozyg mapping model parameters	9.8.5 Autozyg mapping model parameters
	Autozyg MCMC parameters and options	9.8.8 Autozyg MCMC parameters and options
	Autozyg output file description	9.8.4 Autozyg output file description
	Autozyg pedigree file description	9.8.3 Autozyg pedigree file description
	Autozyg population model parameters	9.8.6 Autozyg population model parameters
	Autozyg programs	9.1 Introduction to `lm_auto`, `gl_auto` and `lm_pval`
	Autozyg statements	9.8 Autozyg statements
	autozygosity	9.1 Introduction to `lm_auto`, `gl_auto` and `lm_pval`

B
	base log likelihood	11.6 Parameter files for the `gl_lods` program
	base log likelihood	11.8 Running the `base_trait_lods` program
	`bivar`	13.1 Introduction to PolyEM programs
	block Gibbs sampler	8.4 Single and multiple meiosis LM-samplers
	burn-in	8.5 MCMC computational options
	burn-in	8.6 MCMC parameter statements
	burn-in	9.2 Sample `lm_auto` parameter file

C
	`civil` introduction	10.1 Introduction to `lm_ibdtests` and `civil`
	`civil` sample output	10.5 Sample `civil` output
	`civil` statements	10.6 `lm_ibdtests` and `civil` statements
	Cleopatra pedigree	7.2.3 Selection against autozygosity
	command line options	2.1 Command syntax
	command syntax	2.1 Command syntax
	component	3.1 Introduction to `pedcheck`
	component	3.2 Sample `pedcheck` parameter file
	component	3.5 `pedcheck` statements
	component	4.4 `kin` statements
	conditional ibd probabilities	9. Estimating Conditional ibd Probabilities by MCMC
	consistency (Mendelian) of marker data	9.8.1 Autozyg computing requests
	continuous trait specification	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`

D
	debug control	2.6 Output control
	dense markers	6.1 Introduction to `markerdrop`
	dense markers	7.2.2 Using dense marker simulation
	descent graph	9.1 Introduction to `lm_auto`, `gl_auto` and `lm_pval`
	discrete trait	6.5.4 `markerdrop` computational parameters
	discrete trait	9.8.7 Autozyg computational parameters
	discrete trait specification	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	display –GLUT runtime	2.6 Output control
	display options	2.6 Output control
	dummy statements	2.5 Input extra variables
	dummy statements	4.5 The `translink` utility
	dummy variables	2.5 Input extra variables

E
	EM algorithm	13. Polygenic Modeling of Quantitative Traits by EM Algorithm
	exact computation	9.4 Sample `gl_auto` parameter file
	exact computations	8.3 Exact HMM computations
	examples using pedigree file ‘`ped73.ped`’	1.4 Overview of the pedigrees used in the examples
	extra file	2.3 File identification statements

F
	file names	2.3 File identification statements
	filetype codes	2.1 Command syntax
	founder genome labels	5.1 Introduction to `genedrop`.
	founder genome labels	5.2 Sample `genedrop` parameter file
	founder genome labels	5.4.5 `genedrop` output pedigree options
	founder genome labels	6.4 Running `markerdrop` examples and sample output
	founder genome labels	8.1 Specifying inheritance
	founder genome labels	9.4 Sample `gl_auto` parameter file
	founder genome labels	9.8.4 Autozyg output file description
	founder genome labels (FGL)	6.1 Introduction to `markerdrop`
	fuzzy p-value	9.7 Running `lm_pval` example and sample output

G
	gender–specific maps	5.4.2 `genedrop` mapping model parameters
	gender–specific maps	9.2 Sample `lm_auto` parameter file
	gender–specific maps	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	gender: see also individuals –gender	2.9 Pedigree file description statements
	`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	5.3 Running `genedrop` examples and sample output
	`genedrop` sample parameter file	5.2 Sample `genedrop` parameter file
	`genedrop` statements	5.4 `genedrop` statements
	genetic map estimation	14. Estimating Genetic Maps from Marker Data
	genetic model	8.2 Genetic model
	genotypic trait	9.2 Sample `lm_auto` parameter file
	genotypic trait	9.8.7 Autozyg computational parameters
	genotypic trait specification	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	`gl_auto` introduction	9.1 Introduction to `lm_auto`, `gl_auto` and `lm_pval`
	`gl_auto` sample output	9.5 Running `gl_auto` example and sample output
	`gl_auto` sample parameter file	9.4 Sample `gl_auto` parameter file
	`gl_auto` statements	9.8 Autozyg statements
	`gl_lods` statements	11.9 Location lod scores statements

H
	Haldane map function –See also map function	5.4.2 `genedrop` mapping model parameters
	HMM computations	8.3 Exact HMM computations
	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	4.1 Introduction to `kin`
	ibd	7. Estimating a priori ibd Probabilities by Monte Carlo
	ibd	8.1 Specifying inheritance
	ibd	9. Estimating Conditional ibd Probabilities by MCMC
	ibd graph	4.6 The `ibd_class` utility
	ibd graph	9.1 Introduction to `lm_auto`, `gl_auto` and `lm_pval`
	ibd graph	9.4 Sample `gl_auto` parameter file
	ibd graph	11.6 Parameter files for the `gl_lods` program
	ibd graph	12.1 Introduction to ibd_create and ibd_haplo
	ibd graph	12.5 Running ibd_create examples and sample output; simpop_fgl
	ibd graph	12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
	ibd measures	10.6 `lm_ibdtests` and `civil` statements
	ibd pattern	7.1 Introduction to `ibddrop`
	ibd pattern	7.3 Running `ibddrop` example and sample output
	ibd pattern	9.3 Running `lm_auto` example and sample output
	ibd-based tests	10. Estimating ibd Based Test Statistics by MCMC
	`ibddrop` introduction	7.1 Introduction to `ibddrop`
	`ibddrop` sample output	7.3 Running `ibddrop` example and sample output
	`ibddrop` sample parameter file	7.2 Sample ibddrop parameter file
	`ibddrop` statements	7.4 `ibddrop` statements
	IBDgraph library	4.6 The `ibd_class` utility
	`ibd_class` utility	4.6 The `ibd_class` utility
	`ibd_create` introduction	12.1 Introduction to ibd_create and ibd_haplo
	`ibd_haplo` introduction	12.1 Introduction to ibd_create and ibd_haplo
	identity by descent	7. Estimating a priori ibd Probabilities by Monte Carlo
	identity by descent	9. Estimating Conditional ibd Probabilities by MCMC
	identity by descent	9.1 Introduction to `lm_auto`, `gl_auto` and `lm_pval`
	inbreeding coefficient	4.1 Introduction to `kin`
	inbreeding coefficient	4.4 `kin` statements
	incomplete penetrance	6.5.4 `markerdrop` computational parameters
	incomplete penetrance	9.8.7 Autozyg computational parameters
	incomplete penetrances	6.1 Introduction to `markerdrop`
	individuals –gender	2.9 Pedigree file description statements
	individuals –gender	3.5 `pedcheck` statements
	individuals –names	2.7 Pedigree file
	individuals file	2.3 File identification statements
	individuals file	2.8 Individuals file
	individuals file	3.2 Sample `pedcheck` parameter file
	individuals file	3.4 Creating an `individuals file`
	individuals file	11.6 Parameter files for the `gl_lods` program
	inheritance indicators; See meiosis indicators.	5.4.5 `genedrop` output pedigree options
	inheritance vector	8.1 Specifying inheritance

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