
* ANALYSIS *

AE3                     AE model using nuclear family trios
bt                      Bradley-Terry model for contingency table
ccsize                  Power and sample size for case-cohort design
fbsize                  Sample size for family-based linkage and association design
gc.em                   Gene counting for haplotype analysis
gcontrol                genomic control
gcontrol2               genomic control based on p values
gcp                     Permutation tests using GENECOUNTING
gc.lambda               Estionmation of the genomic control inflation statistic (lambda)
genecounting            Gene counting for haplotype analysis
gif                     Kinship coefficient and genetic index of familiality
hap                     Haplotype reconstruction
hap.em                  Gene counting for haplotype analysis
hap.score               Score statistics for association of traits with haplotypes
htr                     Haplotype trend regression
h2.jags                 Heritability estimation based on genomic relationship matrix using JAGS
hwe                     Hardy-Weinberg equilibrium 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
hwe.jags                Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
invnormal               Inverse normal transformation
kin.morgan              kinship matrix for simple pedigree
LD22                    LD statistics for two diallelic markers
LDkl                    LD statistics for two multiallelic markers
log10p                  log10(p) for a standard normal deviate
masize                  Sample size calculation for mediation analysis
MCMCgrm                 Mixed modeling with genetic relationship matrices
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
mvmeta                  Multivariate meta-analysis based on generalized least squares
pbsize                  Power for population-based association design
pbsize2                 Power for case-control association design
pfc                     Probability of familial clustering of disease
pfc.sim                 Probability of familial clustering of disease
pgc                     Preparing weight for GENECOUNTING
print.hap.score         Print a hap.score object
s2k                     Statistics for 2 by K table
sentinels               Sentinel identification from GWAS summary statistics
tscc                    Power calculation for two-stage case-control design

* GRAPHICS *

asplot                  Regional association plot
ESplot                  Effect-size plot
circos.cnvplot          circos plot of CNVs
circos.cis.vs.trans.plot circos plot of cis/trans classification
circos.mhtplot          circos Manhattan plot with gene annotation
cnvplot                 genomewide plot of CNVs
METAL_forestplot        forest plot as R/meta's forest for METAL outputs
mhtplot                 Manhattan plot
mhtplot2                Manhattan plot with annotations
mhtplot.trunc           truncated Manhattan plot
miamiplot               Miamiplot (Experimental)
pedtodot                Converting pedigree(s) to dot file(s)
plot.hap.score          Plot haplotype frequencies versus haplotype score statistics
qqfun                   Quantile-comparison plots
qqunif                  Q-Q plot for uniformly distributed random variable

* UTILITITES *

SNP                     Functions for single nucleotide polymorphisms (SNPs)
BFDP                    Bayesian false-discovery probability
FPRP                    False-positive report probability
ab                      Test/Power calculation for mediating effect
b2r                     Obtain correlation coefficients and their variance-covariances
chow.test               Chow's test for heterogeneity in two regressions
cis.vs.trans.classification a cis/trans classifier
comp.score              score statistics for testing genetic linkage of quantitative trait
h2                      Heritability estimation according to twin correlations
klem                    Haplotype frequency estimation based on a genotype table
                        of two multiallelic markers
makeped                 A function to prepare pedigrees in post-MAKEPED format
metap                   Meta-analysis of p values
metareg                 Fixed and random effects model for meta-analysis
muvar                   Means and variances under 1- and 2- locus (diallelic) QTL model
read.ms.output          A utility function to read ms output
whscore                 Whittemore-Halpern scores for allele-sharing
GRM functions           ReadGRM, ReadGRMBin, ReadGRMPLINK, ReadGRMPCA, WriteGRM, WriteGRMBin, WriteGRMSAS
                        handle genomic relationship matrix involving other software
heritability functions  h2G, VR, h2GC, h2l give point estimates as with their variances
                        for continuous traits and binary traits under liability threshold model and
                        case-control sampling
