ACDE                    Fit AE, ACE or ADE biometric mixed models to
                        nuclear family data
AE3                     AE model using nuclear family trios
BFDP                    Bayesian false-discovery probability
ESplot                  Effect-size / Odds-ratio forest plot
FPRP                    False-positive report probability
KCC                     Disease prevalences in cases and controls
LD22                    LD statistics for two diallelic markers
LDkl                    LD statistics for two multiallelic markers
MCMCgrm                 Mixed modeling with genetic relationship
                        matrices
METAL_forestplot        forest plot as R/meta's forest for METAL
                        outputs
ReadGRM                 A function to read GRM file
ReadGRMBin              A function to read GRM binary files
WriteGRM                A function to write GRM file
WriteGRMBin             A function to write GRM binary file
a2g                     Allele-to-genotype conversion
ab                      Test/Power calculation for mediating effect
allele.recode           Allele recoding
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
chow.test               Chow's test for heterogeneity in two
                        regressions
chr_pos_a1_a2           SNP id by chr:pos+a1/a2
ci2ms                   Effect size and standard error from confidence
                        interval
circos.cis.vs.trans.plot
                        circos plot of cis/trans classification
circos.cnvplot          circos plot of CNVs.
circos.mhtplot          circos Manhattan plot with gene annotation
circos.mhtplot2         Another circos Manhattan plot
cis.vs.trans.classification
                        A cis/trans classifier
cnvplot                 genomewide plot of CNVs
comp.score              score statistics for testing genetic linkage of
                        quantitative trait
cs                      Credible set from summary statistics
fbsize                  Sample size for family-based linkage and
                        association design
g2a                     Conversion of a genotype identifier to alleles
gc.em                   Gene counting for haplotype analysis
gc.lambda               Estimation of the genomic control inflation
                        statistic (lambda)
gcontrol                genomic control
gcontrol2               genomic control based on p values
gcp                     Permutation tests using GENECOUNTING
genecounting            Gene counting for haplotype analysis
geno.recode             Genotype recoding
get_b_se                Get b and se from AF, n, and z
get_pve_se              Get pve and its standard error from n, z
get_sdy                 Get sd(y) from AF, n, b, se
gif                     Kinship coefficient and genetic index of
                        familiality
grid2d                  Two-dimensional grid
h2.jags                 Heritability estimation based on genomic
                        relationship matrix using JAGS
h2G                     Heritability and its variance
h2GE                    Heritability and its variance when there is an
                        environment component
h2_mzdz                 Heritability estimation according to twin
                        correlations
h2l                     Heritability under the liability threshold
                        model
hap                     Haplotype reconstruction
hap.control             Control for haplotype reconstruction
hap.em                  Gene counting for haplotype analysis
hap.score               Score statistics for association of traits with
                        haplotypes
hg18                    Chromosomal lengths for build 36
hg19                    Chromosomal lengths for build 37
hg38                    Chromosomal lengths for build 38
hmht.control            Controls for highlighted regions in mhtplot
htr                     Haplotype trend regression
hwe                     Hardy-Weinberg Equilibrium Test (Multiallelic,
                        Unified Interface)
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
inv_chr_pos_a1_a2       Retrieval of chr:pos+a1/a2 according to SNP id
invnormal               Inverse normal transformation
ixy                     Conversion of chrosome name from strings
kin.morgan              kinship matrix for simple pedigree
klem                    Haplotype frequency estimation based on a
                        genotype table of two multiallelic markers
labelManhattan          Annotate Manhattan or Miami Plot
log10p                  log10(p) for a normal deviate z
log10pvalue             log10(p) for a P value including its scientific
                        format
logp                    log(p) for a normal deviate z
makeped                 A function to prepare pedigrees in post-MAKEPED
                        format
masize                  Sample size calculation for mediation analysis
metap                   Meta-analysis of p-values with heterogeneity
                        and random effects
metareg                 Fixed and random effects meta-analysis
                        (vectorised implementation)
mht.control             Controls for Manhattan plot
mhtplot                 Manhattan plot
mhtplot.trunc           Truncated Manhattan plot
mhtplot2                Manhattan plot with annotations
mia                     Multiple imputation analysis for hap
miamiplot               Miami plot
miamiplot2              Miami Plot
mr                      Mendelian Randomization wrapper (IVW, Egger,
                        Weighted Median, Penalised WM)
mr_forestplot           Mendelian Randomization forest plot
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 fixed-effects meta-analysis via
                        generalized least squares
pbsize                  Power for population-based association design
pbsize2                 Power for case-control association design
pedtodot                Converting pedigree(s) to dot file(s)
pedtodot_verbatim       Pedigree-drawing with graphviz
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
pvalue                  P value for a normal deviate
qqfun                   Quantile-comparison plots
qqunif                  Q-Q plot for uniformly distributed random
                        variables
qtl2dplot               2D QTL plot
qtl2dplotly             2D QTL plotly
qtl3dplotly             3D QTL plot
qtlClassifier           A QTL cis/trans classifier
qtlFinder               Distance-based signal identification
read.ms.output          A utility function to read ms output
revStrand               Allele on the reverse strand
runshinygap             Start shinygap
s2k                     Statistics for 2 by K table
sentinels               Sentinel identification from GWAS summary
                        statistics
snpHWE                  Functions for single nucleotide polymorphisms
snptest_sample          A utility to generate SNPTEST sample file
tscc                    Power calculation for two-stage case-control
                        design
whscore                 Whittemore-Halpern scores for allele-sharing
xy                      Conversion of chromosome names to strings
