BFDP                    Bayesian false-discovery probability
CDKN                    Example data for association plot
ESplot                  Effect-size plot
FPRP                    False-positive report probability
LD22                    LD statistics for two diallelic markers
LDkl                    LD statistics for two multiallelic markers
SNP                     Functions for single nucleotide polymorphisms
                        (SNPs)
ab                      Test/Power calculation for mediating effect
aldh2                   ALDH2 markers and Alcoholism
apoeapoc                APOE/APOC1 markers and Alzheimer's
asplot                  Regional association plot
b2r                     Obtain correlation coefficients and their
                        variance-covariances
bt                      Bradley-Terry model for contingency table
ccsize                  Power and sample size for case-cohort design
cf                      Cystic fibrosis data
chow.test               Chow's test for heterogeneity in two
                        regressions
comp.score              score statistics for testing genetic linkage of
                        quantitative trait
crohn                   Crohn's disease data
fa                      Friedreich Ataxia data
fbsize                  Sample size for family-based linkage and
                        association design
fsnps                   A case-control data involving four SNPs with
                        missing genotype
gap-package             Genetic analysis package
gc.em                   Gene counting for haplotype analysis
gcontrol                genomic control
gcontrol2               genomic control based on p values
gcp                     Permutation tests using GENECOUNTING
genecounting            Gene counting for haplotype analysis
gif                     Kinship coefficient and genetic index of
                        familiality
h2                      Heritability estimation according to twin
                        correlations
hap                     Haplotype reconstruction
hap.em                  Gene counting for haplotype analysis
hap.score               Score statistics for association of traits with
                        haplotypes
hla                     The HLA data
htr                     Haplotype trend regression
hwe                     Hardy-Weinberg equlibrium test for a
                        multiallelic marker
hwe.cc                  A likelihood ratio test of population
                        Hardy-Weinberg equilibrium for case-control
                        studies
hwe.hardy               Hardy-Weinberg equilibrium test using MCMC
kin.morgan              kinship matrix for simple pedigree
klem                    Haplotype frequency estimation based on a
                        genotype table of two multiallelic markers
makeped                 A function to prepare pedigrees in post-MAKEPED
                        format
mao                     A study of Parkinson's disease and MAO gene
masize                  Sample size calculation for mediation analysis
metap                   Meta-analysis of p values
metareg                 Fixed and random effects model for
                        meta-analysis
mhtplot                 Manhattan plot of p values
mia                     multiple imputation analysis for hap
mtdt                    Transmission/disequilibrium test of a
                        multiallelic marker
mtdt2                   Transmission/disequilibrium test of a
                        multiallelic marker by Bradley-Terry model
muvar                   Means and variances under 1- and 2- locus
                        (biallelic) QTL model
mvmeta                  Multivariate meta-analysis based on generalized
                        least squares
nep499                  A study of Alzheimer's disease with eight SNPs
                        and APOE
pbsize                  Power for population-based association design
pbsize2                 Power for case-control association design
pedtodot                Converting pedigree(s) to dot file(s)
pfc                     Probability of familial clustering of disease
pfc.sim                 Probability of familial clustering of disease
pgc                     Preparing weight for GENECOUNTING
plot.hap.score          Plot haplotype frequencies versus haplotype
                        score statistics
print.hap.score         Print a hap.score object
qqfun                   Quantile-comparison plots
qqunif                  Q-Q plot for uniformly distributed random
                        variable
read.ms.output          A utility function to read ms output
s2k                     Statistics for 2 by K table
snca                    A study of Parkinson's disease and SNCA makers
tscc                    Power calculation for two-stage case-control
                        design
twinan90                Classic twin models
whscore                 Whittemore-Halpern scores for allele-sharing
