Concept Index: N – S

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	Index Entry	Section

N
	names; See individuals –names	2.7 Pedigree file
	non-genetic model	5.1 Introduction to `genedrop`.

O
	observed individuals	2.7 Pedigree file
	observed individuals	13.4.3 `multivar` computational parameters
	output –redirect	2.6 Output control
	output control	2.6 Output control
	output warnings (W)	2.6 Output control
	overview of MORGAN	1.1 Overview of MORGAN
	overwrite file options	2.3 File identification statements
	overwrite file options	3.2 Sample `pedcheck` parameter file

P
	parameter file	2.2 Parameter file
	parameter statement flexibility	2.2 Parameter file
	parameter statements	2.2 Parameter file
	parameter statements in pedigree files	2.7 Pedigree file
	`pedcheck` examples	3.3 Running `pedcheck` examples
	`pedcheck` introduction	3.1 Introduction to `pedcheck`
	`pedcheck` sample parameter file	3.2 Sample `pedcheck` parameter file
	`pedcheck` statements	3.5 `pedcheck` statements
	pedigree component –See component	3.1 Introduction to `pedcheck`
	pedigree file	2.3 File identification statements
	pedigree file	2.7 Pedigree file
	pedigree file descriptions	2.9 Pedigree file description statements
	pedigree file separator	2.7 Pedigree file
	pedigree options	3.5 `pedcheck` statements
	pedigree order	3.5 `pedcheck` statements
	pedigree peeling	8.4 Single and multiple meiosis LM-samplers
	pedigree record format	2.9 Pedigree file description statements
	pedigree record format	6.5.5 `markerdrop` input file options
	pedigree size	2.9 Pedigree file description statements
	pedigree trait integer data order	2.9 Pedigree file description statements
	pedigree trait real data order	2.9 Pedigree file description statements
	pedigree validity	3.1 Introduction to `pedcheck`
	penetrance	6.5.4 `markerdrop` computational parameters
	penetrance	8.2 Genetic model
	permutation based base-lod	11.9.7 Location lod scores computational parameters
	phased and unphased genotypes	6.4 Running `markerdrop` examples and sample output
	phased and unphased genotypes	8.4 Single and multiple meiosis LM-samplers
	phased and unphased genotypes	12.7 Running ibd_create examples and sample output; fgl2ibd and fgl2haplo and fgl2dgl
	phased and unphased haplotypes	12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
	phenotypic trait specification	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	PolyEM	13. Polygenic Modeling of Quantitative Traits by EM Algorithm
	PolyEM introduction	13.1 Introduction to PolyEM programs
	PolyEM statements	13.4 `multivar` statements
	polygenic model	5.1 Introduction to `genedrop`.
	polygenic model	13. Polygenic Modeling of Quantitative Traits by EM Algorithm
	population kinship	12.8 Sample parameter files for ibd_haplo
	population kinship	12.10.4 ibd_haplo parameter statements
	population-based IBD inference	12. Population-based inference of IBD
	population-based IBD inference parameter statements	12.10 Population-based IBD inference parameter statements
	printlevel control	2.6 Output control
	printlevel control	6.2 Sample `markerdrop` parameter file – conditional on trait
	proband gametes	7.2.1 Classic ibddrop parameter file
	proband gametes	7.4 `ibddrop` statements
	proband gametes	9.2 Sample `lm_auto` parameter file
	proband gametes	9.3 Running `lm_auto` example and sample output
	proband gametes	9.8.7 Autozyg computational parameters
	proband gametes	12.1 Introduction to ibd_create and ibd_haplo
	proband gametes	12.10.4 ibd_haplo parameter statements
	pseudo-prior iterations	8.5 MCMC computational options
	pseudo-prior iterations	11.9.7 Location lod scores computational parameters

Q
	quantitative trait	5.1 Introduction to `genedrop`.
	quantitative trait	9.8.7 Autozyg computational parameters
	quantitative trait	11.9.3 Location lod scores pedigree file description
	quantitative trait	13. Polygenic Modeling of Quantitative Traits by EM Algorithm
	quantitative trait specification	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`

R
	randomized p-values	10.4 Sample `civil` parameter file
	Rao-Blackwellized estimates	11.4 Running `lm_bayes` examples and sample output
	Rao-Blackwellized estimates	11.9.2 Location lod scores file identification statements
	README documentation files	1.5 Structure of the MORGAN package
	recombination	4.4 `kin` statements
	recombination breakpoints	6.5.1 `markerdrop` computing requests
	recombination breakpoints	7.4 `ibddrop` statements
	rescue file	9.8.2 Autozyg file identification statements
	residual variance	5.2 Sample `genedrop` parameter file
	residual variance	5.4.3 `genedrop` population model parameters
	running `beaglesim` and `beagledag`	12.3 Running ibd_create examples and sample output; beaglesim and beagledag
	running `fgl2ibd`, `fgl2haplo` and `fgl2dgl`	12.7 Running ibd_create examples and sample output; fgl2ibd and fgl2haplo and fgl2dgl
	running `genedrop` examples	5.3 Running `genedrop` examples and sample output
	running `gl_auto` example	9.5 Running `gl_auto` example and sample output
	running `ibddrop` example	7.3 Running `ibddrop` example and sample output
	running `kin` example	4.3 Running `kin` example and sample output
	running `lm_auto` example	9.3 Running `lm_auto` example and sample output
	running `lm_bayes` examples	11.4 Running `lm_bayes` examples and sample output
	running `lm_linkage` examples	11.3 Running `lm_linkage` examples and sample output
	running `lm_map` with genotypic data	14.3 Running `lm_map` with genotypic data
	running `lm_map` with phenotypic data	14.4 Running `lm_map` with phenotypic data
	running `lm_pval` example	9.7 Running `lm_pval` example and sample output
	running `lm_twoqtl` examples	11.5 Running `lm_twoqtl` examples and sample output
	running `markerdrop` examples	6.4 Running `markerdrop` examples and sample output
	running `multivar` example	13.3 Running multivar example and sample output
	running `simpop_fgl`	12.5 Running ibd_create examples and sample output; simpop_fgl

S
	sample by scan	8.5 MCMC computational options
	sample by scan	8.6 MCMC parameter statements
	sample by step	8.5 MCMC computational options
	sample by step	8.6 MCMC parameter statements
	sample parameter file for `beaglesim` and `beagledag`	12.2 Sample parameter files for ibd_create; `beaglesim` and `beagledag`
	sample parameter file for `civil`	10.4 Sample `civil` parameter file
	sample parameter file for `ibd_haplo`	12.8 Sample parameter files for ibd_haplo
	sample parameter file for `lm_bayes`	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	sample parameter file for `lm_ibdtests`	10.2 Sample `lm_ibdtests` parameter file
	sample parameter file for `lm_linkage`	11.2 Sample parameter files for `lm_linkage` and `lm_bayes`
	sample parameter file for `lm_map`	14.2 Sample `lm_map` parameter file
	sample parameter file for `simpop_fgl`	12.4 Sample parameter files for ibd_create; simpop_fgl
	sample parameter files for `fgl2ibd`, `fgl2haplo` and `fgl2dgl`	12.6 Sample parameter files for ibd_create; fgl2ibd and fgl2haplo and fgl2dgl
	score file	9.8.2 Autozyg file identification statements
	scoreset	9.8.7 Autozyg computational parameters
	scoreset	12.10.4 ibd_haplo parameter statements
	seed file	2.3 File identification statements
	seed file	5.2 Sample `genedrop` parameter file
	seed file	7.2.1 Classic ibddrop parameter file
	seeds for data simulation	5.1 Introduction to `genedrop`.
	seeds for data simulation	5.3 Running `genedrop` examples and sample output
	seeds for data simulation	5.4.4 `genedrop` computational parameters
	seeds for data simulation	5.4.6 `genedrop` output seed file options
	seeds for sampler	7.2.1 Classic ibddrop parameter file
	seeds for sampler	7.4 `ibddrop` statements
	selection against autozygosity	7.2.3 Selection against autozygosity
	selection against maternal identity	7.2.3 Selection against autozygosity
	sequential imputation	8.5 MCMC computational options
	sequential imputation	8.6 MCMC parameter statements
	sequential imputation proposals	11.9.8 Location lod scores MCMC parameters and options
	simulating marker and trait data	5. Simulating Marker and Trait Data in Pedigrees
	simulating marker and trait data	5.4.4 `genedrop` computational parameters
	simulation of a population	12.4 Sample parameter files for ibd_create; simpop_fgl
	simulation of descent in a pedigree	7.1 Introduction to `ibddrop`
	simulation of descent in a pedigree	12.4 Sample parameter files for ibd_create; simpop_fgl
	specifying inheritance	8.1 Specifying inheritance
	state ordering: Jacquard	12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
	state ordering: Jacquard	12.10.4 ibd_haplo parameter statements
	state ordering: lexicographic	12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements

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