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gap (version 1.0-8)

Genetic analysis package

Description

This is an integrated package for genetic data analysis of both population and family data. Currently it contains functions for sample size calculations of both population-based and family-based designs, classic twin ACE/ADE/AE/CE models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

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Version

Install

install.packages('gap')

Monthly Downloads

20,276

Version

1.0-8

License

Programs included in this package by Jing Hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors.

Maintainer

Jing Zhao

Last Published

February 6th, 2026

Functions in gap (1.0-8)

internal functions for gap

APOE/APOC1 markers and Schizophrenia

Cystic Fibrosis data

kinship matrix for simple pedigree

Chow's test for heterogeneity in two regressions

A case-control data involving four SNPs with missing genotype

ALDH2 markers and Alcoholism

genomic control

Score statistics for association of traits with haplotypes

Gene counting for haplotype analysis

Power for population-based association design

Probability of familial clustering of disease

Friedreich Ataxia data

Haplotype reconstruction

A function to prepare pedigrees in post-MAKEPED format

Transmission/disequilibrium test of a multiallelic marker

A study of Parkinson's disease and MAO gene

LD statistics for two multiallelic loci

Sample size for family-based linkage and association design

Permutation tests using GENECOUNTING

Statistics for 2 by K table

Probability of familial clustering of disease

Classic twin models

print.hap.score

Print a hap.score object

A study of Parkinson's disease and SNCA makers

LD statistics for two SNPs

Whittemore-Halpern scores for allele-sharing

Hardy-Weinberg equlibrium test for multiallelic marker

Hardy-Weinberg equilibrium test using MCMC

Crohn disease data

Power and sample size for case-cohort design

A study of Alzheimer's disease with eight SNPs and APOE

Kinship coefficient and genetic index of familiality

Means and variances under 1- and 2- locus (biallelic) QTL model

Plot Haplotype Frequencies versus Haplotype Score Statistics

Haplotype trend regression

multiple imputation analysis for hap

Converting pedigree(s) to dot file(s)

Preparing weight for GENECOUNTING

Bradley-Terry model for contingency table

Gene counting for haplotype analysis

Gene counting for haplotype analysis