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