Index: BFDP Bayesian false-discovery probability FPRP False-positive report probability SNP Functions for single nucleotide polymorphisms (SNPs) abc Test/Power calculation for mediating effect aldh2 ALDH2 markers and Alcoholism apoeapoc APOE/APOC1 markers and Schizophrenia asplot Regional association plot bt Bradley-Terry model for contingency table b2r Obtain correlation coefficients and their variance-covariances ccsize Power and sample size for case-cohort design chow.test Chow's test for heterogeneity in two regressions cf Cystic Fibrosis data comp.score score statistics for testing genetic linkage of quantitative trait crohn Crohn disease data ESplot Effect-size plot fa Friedreich Ataxia data fbsize Sample size for family-based linkage and association design fsnps A case-control data involving four SNPs with missing genotype 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 hap Haplotype reconstruction hap.em Gene counting for haplotype analysis hap.score Score Statistics for Association of Traits with Haplotypes hla HLA markers and Schizophrenia htr Haplotype trend regression hwe Hardy-Weinberg equlibrium test for multiallelic marker hwe.hardy Hardy-Weinberg equlibrium test using MCMC kin.morgan kinship matrix for simple pedigree LD22 LD statistics for two diallelic markers LDkl LD statistics for two multiallelic markers makeped A function to prepare pedigrees in post-MAKEPED format mao A study of Parkinson's disease and MAO gene metap Meta-analysis of p values metareg Fixed and random effects model for meta-analysis mhtplot Manhattan plot of p values mia multiple imputation analysis for hap mtdt Transmission/disequilibrium test of a multiallelic marker muvar Means and variances under 1- and 2- locus (diallelic) QTL model mvmeta Multivariate meta-analysis based on generalized least squares nep499 A study of Alzheimer's disease with eight SNPs and APOE 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 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 snca A study of Parkinson's disease and SNCA makers tscc Power calculation for two-stage case-control design twinan90 Classic twin models whscore Whittemore-Halpern scores for allele-sharing
We have incorporated functions for a wide range of problems. Nevertheless, this largely remains as a preliminary work to be consolidated in the near future.