| a2g | Allele-to-genotype conversion |
| ab | Test/Power calculation for mediating effect |
| AE3 | AE model using nuclear family trios |
| allele.recode | Allele recoding |
| asplot | Regional association plot |
| b2r | Obtain correlation coefficients and their... |
| 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 |
| 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... |
| cs | Credible set |
| ESplot | Effect-size plot |
| fbsize | Sample size for family-based linkage and association design |
| FPRP | False-positive report probability |
| g2a | Conversion of a genotype identifier to alleles |
| gap | Genetic analysis package |
| gc.em | Gene counting for haplotype analysis |
| gc.lambda | Estimation of the genomic control inflation statistic... |
| 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 |
| h2G | Heritability and its variance |
| h2GE | Heritability and its variance when there is an environment... |
| h2.jags | Heritability estimation based on genomic relationship matrix... |
| h2l | Heritability under the liability threshold model |
| h2_mzdz | Heritability estimation according to twin correlations |
| 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 highlights |
| htr | Haplotype trend regression |
| hwe | Hardy-Weinberg equlibrium test for a multiallelic marker |
| hwe.cc | A likelihood ratio test of population Hardy-Weinberg... |
| hwe.hardy | Hardy-Weinberg equilibrium test using MCMC |
| hwe.jags | Hardy-Weinberg equlibrium test for a multiallelic marker... |
| 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 |
| KCC | Disease prevalences in cases and controls |
| kin.morgan | kinship matrix for simple pedigree |
| klem | Haplotype frequency estimation based on a genotype table of... |
| labelManhattan | Annotate Manhattan or Miami Plot |
| LD22 | LD statistics for two diallelic markers |
| LDkl | LD statistics for two multiallelic markers |
| 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 |
| 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 |
| mht.control | Controls for mhtplot |
| mhtplot | Manhattan plot |
| mhtplot2 | Manhattan plot with annotations |
| mhtplot.trunc | Truncated Manhattan plot |
| mia | Multiple imputation analysis for hap |
| miamiplot | Miami plot |
| miamiplot2 | Miami Plot |
| mr | Mendelian randomization analysis |
| mr_forestplot | Mendelian Randomization forest plot |
| mtdt | Transmission/disequilibrium test of a multiallelic marker |
| mtdt2 | Transmission/disequilibrium test of a multiallelic marker by... |
| muvar | Means and variances under 1- and 2- locus (biallelic) QTL... |
| 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) |
| 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 variable |
| qtl2dplot | 2D QTL plot |
| qtl2dplotly | 2D QTL plotly |
| qtl3dplotly | 3D QTL plot |
| qtlClassifier | A QTL cis/trans classifier |
| qtlFinder | Distance-based signal identification |
| ReadGRM | A function to read GRM file |
| ReadGRMBin | A function to read GRM binary files |
| 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 |
| SNP | 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 |
| WriteGRM | A function to write GRM file |
| WriteGRMBin | A function to write GRM binary file |
| xy | Conversion of chromosome names to strings |
