| gap-package | Genetic analysis package |
| ab | Test/Power calculation for mediating effect |
| AE3 | AE model using nuclear family trios |
| asplot | Regional association plot |
| b2r | Obtain correlation coefficients and their variance-covariances |
| BFDP | Bayesian false-discovery probability |
| 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 |
| comp.score | score statistics for testing genetic linkage of quantitative trait |
| ESplot | Effect-size plot |
| fbsize | Sample size for family-based linkage and association design |
| FPRP | False-positive report probability |
| gap | 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 |
| h2.jags | Heritability estimation based on genomic relationship matrix using JAGS |
| hap | Haplotype reconstruction |
| hap.em | Gene counting for haplotype analysis |
| hap.score | Score statistics for association of traits with haplotypes |
| 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 |
| hwe.jags | Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS |
| kin.morgan | kinship matrix for simple pedigree |
| klem | Haplotype frequency estimation based on a genotype table of two multiallelic markers |
| LD22 | LD statistics for two diallelic markers |
| LDkl | LD statistics for two multiallelic markers |
| makeped | A function to prepare pedigrees in post-MAKEPED format |
| masize | Sample size calculation for mediation analysis |
| MCMCgrm | Mixed modeling with genetic relationship matrices |
| METAL_forestplot | forest plot as R/meta's forest for METAL outputs |
| metap | Meta-analysis of p values |
| metareg | Fixed and random effects model for meta-analysis |
| mhtplot | Manhattan plot |
| mhtplot.trunc | Truncated Manhattan plot |
| mhtplot2 | Manhattan plot with annotations |
| 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 |
| 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 |
| pm | Permutation tests using GENECOUNTING |
| pmplus | Permutation tests using GENECOUNTING |
| 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 |
| sentinels | Sentinel identification from GWAS summary statistics |
| SNP | Functions for single nucleotide polymorphisms (SNPs) |
| snp.ES | Functions for single nucleotide polymorphisms (SNPs) |
| snp.HWE | Functions for single nucleotide polymorphisms (SNPs) |
| snp.PAR | Functions for single nucleotide polymorphisms (SNPs) |
| tscc | Power calculation for two-stage case-control design |
| whscore | Whittemore-Halpern scores for allele-sharing |