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