* ANALYSIS * AE3 AE model using nuclear family trios bt Bradley-Terry model for contingency table ccsize Power and sample size for case-cohort design cs Credible set 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 gsmr Mendelian randomization analysis 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 lambda1000 A standardized estimate of the genomic inflation scaling to a study of 1,000 cases and 1,000 controls log10p log10(p) for a normal deviate log10pvalue log10(p) for a P value including its scientific format logp log(p) for a 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 makeRLEplot make relative log expression plot mhtplot Manhattan plot mhtplot2 Manhattan plot with annotations pqtl2dplot 2D pQTL plot pqtl2dplotly 2D pQTL plotly pqtl3dplotly 3D pQTL plotly mhtplot.trunc truncated Manhattan plot miamiplot Miami plot 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 chr_pos_a1_a2 Form SNPID from chromosome, posistion and alleles cis.vs.trans.classification A cis/trans classifier comp.score score statistics for testing genetic linkage of quantitative trait GRM functions ReadGRM, ReadGRMBin, ReadGRMPLINK, ReadGRMPCA, WriteGRM, WriteGRMBin, WriteGRMSAS handle genomic relationship matrix involving other software 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 h2G A utility function for heritability h2GE A utility function for heritability involving gene-environment interaction h2l A utility function for converting observed heritability to its counterpart under liability threshold model h2_mzdz 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 pvalue P value for a normal deviate read.ms.output A utility function to read ms output revStrand Allele on the reverse strand runshinygap Start shinygap snptest_sample A utility to generate SNPTEST sample file weighted.median Weighted median with interpolation whscore Whittemore-Halpern scores for allele-sharing