Genetic analysis package
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
Gene counting for haplotype analysis
Example data for ACEnucfam
Print a hap.score object
Test/Power calculation for mediating effect
Haplotype trend regression
Quantile-comparison plots
LD statistics for two diallelic markers
Permutation tests using GENECOUNTING
Sample size calculation for mediation analysis
Regional association plot
Example data for association plot
Effect-size plot
False-positive report probability
APOE/APOC1 markers and Alzheimer's
LD statistics for two multiallelic markers
Chow's test for heterogeneity in two regressions
Crohn's disease data
Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model
Multivariate meta-analysis based on generalized least squares
Manhattan plot of p values
The HLA data
Gene counting for haplotype analysis
Whittemore-Halpern scores for allele-sharing
A case-control data involving four SNPs with missing genotype
Gene counting for haplotype analysis
score statistics for testing genetic linkage of quantitative trait
Classic twin models
Bradley-Terry model for contingency table
Internal functions for gap
Cystic fibrosis data
A study of Parkinson's disease and MAO gene
Bayesian false-discovery probability
Obtain correlation coefficients and their variance-covariances
Power for case-control association design
Haplotype reconstruction
Functions for single nucleotide polymorphisms (SNPs)
Fixed and random effects model for meta-analysis
A study of Alzheimer's disease with eight SNPs and APOE
Kinship coefficient and genetic index of familiality
Heritability estimation according to twin correlations
genomic control
Plot haplotype frequencies versus haplotype score statistics
kinship matrix for simple pedigree
A utility function to read ms output
A study of Parkinson's disease and SNCA makers
Sample size for family-based linkage and association design
An example data for Manhattan plot
Means and variances under 1- and 2- locus (biallelic) QTL model
Score statistics for association of traits with haplotypes
A function to prepare pedigrees in post-MAKEPED format
Power and sample size for case-cohort design
Hardy-Weinberg equilibrium test using MCMC
Friedreich Ataxia data
An example data for Manhattan plot with annotation
Haplotype frequency estimation based on a genotype table of two multiallelic markers
Meta-analysis of p values
Hardy-Weinberg equlibrium test for a multiallelic marker
Power for population-based association design
genomic control based on p values
multiple imputation analysis for hap
A study of Parkinson's disease and APOE, LRRK2, SNCA makers
An example pedigree
Probability of familial clustering of disease
ALDH2 markers and Alcoholism
Transmission/disequilibrium test of a multiallelic marker
Statistics for 2 by K table
An example pedigree data
Converting pedigree(s) to dot file(s)
Manhattan plot with annotations
Probability of familial clustering of disease
Q-Q plot for uniformly distributed random variable
Power calculation for two-stage case-control design
Preparing weight for GENECOUNTING
AE model using nuclear family trios
A pedigree data on 282 animals deriving from two generations
Mixed modeling with genetic relationship matrices