PAP Manual - Contents
TABLE OF CONTENTS
I. INTRODUCTION
II. PREPARING THE INPUT FILES
II.1. Pedigree Structure: trip.dat
II.2. Computation Order: order.dat
II.3. Marker/Trait Descriptions: header.dat
II.4. Phenotype Data: phen.dat, ascer.dat
II.5. Population Information: popln.dat
III. USING THE PROGRAMS
III.1. Data Preparation Program: preped
III.2. Descriptive Statistics Program: descstat
III.3. Analysis Preparation Program: prepap
III.4. Simulation Program: simul
III.5. Analysis Program: papdr
III.6. Estimation Program: gpe
IV. DEFINING THE MODEL
IV.1. Execution Options
IV.1.1. Single likelihood
IV.1.2. Genotypic probabilities
IV.1.3. Simulation and output to files
IV.1.4. Maximization of parameters
IV.1.5. Standard errors of parameters
IV.1.6. Simulation and estimation
IV.1.7. Expected lod score estimation
IV.1.8. Grid on a parameter
IV.2. Transmission Parameters
IV.2.1. Mendelian segregation
IV.2.2. Environmental nontransmission
IV.2.3. General transmission
IV.3. Recombination Parameters
IV.4. Frequency Parameters
IV.4.1. Allele frequencies
IV.4.2. Conditional allele frequencies
IV.4.3. Haplotype frequencies
IV.4.4. Genotype frequencies
IV.5. Discrete Trait Parameters
IV.5.1. Affection probability
IV.5.2. Prevalence
IV.5.3. Incidence
IV.5.4. Severity Classes
IV.6. Quantitative Trait Parameters
IV.6.1. Means/Standard Deviations
IV.6.2. Dominance/Displacement
IV.6.3. Means/Standard Deviations/Threshold
IV.7. Within-Genotype Parameters
IV.8. Multivariate Parameters
IV.9. Genotype-Assignment Codes
IV.9.1. Autosomal inheritance
IV.9.2. X-linked inheritance
IV.9.3. Parent-specific autosomal
IV.9.4. Parent-specific X-linked
IV.9.5. Category-specific autosomal
IV.9.6. Autosomal/X-linked mixed model
IV.9.7. Autosomal/X-linked admixture
V. PERFORMING THE ANALYSIS
V.1. Preparing for the Analysis
V.2. Checking for Errors
V.2.1. Performing preliminary tests
V.2.2. Verifying analysis results
V.3. Maximizing the Likelihoods
V.3.1. Finding the global maximum
V.3.2. Determining when a maximum occurs on the boundary
V.4. Interpreting the Results
VI. UNDERSTANDING THE PACKAGE
VI.1. Computation Order
VI.2. Genotype Order
VI.3. Genotype Combining
VI.4. Ascertainment Correction
VI.5. Use of Logarithms
VI.6. Likelihood Calculation
VI.7. Genotypic Probabilities
VI.8. Penetrance Probabilities
VI.9. Genotype Simulation
VI.10. Conditioning Process
VII. WRITING CUSTOM SUBROUTINES
VII.1. Frequency: papfq
VII.2. Transmission: paptc
VII.3. Major Locus Discrete: dmlpr
VII.4. Major Locus Quantitative: qmlpr
VII.5. Within Genotype: papwg
VIII. ACKNOWLEDGMENTS
IX. REFERENCES
A. FILE LISTS
A.1. Command Files
A.2. Include Files
A.3. Source Files
A.4. Input Files
A.5. Test Data Files
A.6. Parameter Files
A.7. Output Files
B. FILE FORMATS
B.1. Pedigree Structure: trip.dat (see section II.1)
B.2. Computation Order: order.dat (see section II.2)
B.3. Trait/Marker Descriptions: header.dat (see section II.3)
B.4. Phenotype Data: phen.dat and ascer.dat (see section II.4)
B.5. Population Information: popln.dat (see section II.5)
B.6. Pedigree and Phenotype Data: papin.dat (written by preped (section III.1))
B.7. Model and Parameter Information: model.dat (written by prepap (section III.3))
B.8. Frequency Subroutine List: freq.dat
B.9. Transmission Subroutine List: tran.dat
B.11. Major Locus Quantitative Subroutine List: qmlp.dat
B.12. Within Genotype Subroutine List: wgen.dat
C. SUBROUTINE LIBRARIES
C.1. Frequency: papfq
C.2. Transmission: paptc
C.3. Major Locus Discrete: dmlpr
C.4. Major Locus Quantitative: qmlpr
C.5. Within Genotype: papwg
D. TEST EXAMPLES
D.1. Execution Options
D.2. Transmission Parameters
D.4. Frequency Parameters
D.5. Discrete Trait Parameters
D.6. Quantitative Trait Parameters
D.7. Within-Genotype Parameters
D.8. Multivariate Parameters
D.9. Genotype-Assignment Codes
E. ERROR MESSAGES
E.1. Errors in the Files: filerr
E.2. Errors in the Data Files: daterr
E.3. Errors in the Genetic Model: moderr
E.4. Execution Errors: paperr
F. CHANGES FROM REVISION 3
F.1. Files
F.2. Programs
F.3. Genetic Models
F.4. Algorithms
