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