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gap (version 1.0-9)

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

1.0-9

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 (1.0-9)

cf

Cystic Fibrosis data
nep499

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

Transmission/disequilibrium test of a multiallelic marker
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
hap.em

Gene counting for haplotype analysis
fa

Friedreich Ataxia data
aldh2

ALDH2 markers and Alcoholism
gc.em

Gene counting for haplotype analysis
htr

Haplotype trend regression
print.hap.score

Print a hap.score object
gcontrol

genomic control
mao

A study of Parkinson's disease and MAO gene
hla

The HLA data
crohn

Crohn disease data
pedtodot

Converting pedigree(s) to dot file(s)
kin.morgan

kinship matrix for simple pedigree
bt

Bradley-Terry model for contingency table
kbyl

LD statistics for two multiallelic loci
twinan90

Classic twin models
makeped

A function to prepare pedigrees in post-MAKEPED format
fsnps

A case-control data involving four SNPs with missing genotype
pbsize

Power for population-based association design
hap

Haplotype reconstruction
genecounting

Gene counting for haplotype analysis
muvar

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

Power calculation for two-stage case-control design
hwe

Hardy-Weinberg equlibrium test for multiallelic marker
pfc

Probability of familial clustering of disease
tbyt

LD statistics for two SNPs
gif

Kinship coefficient and genetic index of familiality
pfc.sim

Probability of familial clustering of disease
plot.hap.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
gcp

Permutation tests using GENECOUNTING
apoeapoc

APOE/APOC1 markers and Schizophrenia
chow.test

Chow's test for heterogeneity in two regressions
hap.score

Score statistics for association of traits with haplotypes
mia

multiple imputation analysis for hap
ccsize

Power and sample size for case-cohort design
fbsize

Sample size for family-based linkage and association design
gap-internal

internal functions for gap
pgc

Preparing weight for GENECOUNTING
snca

A study of Parkinson's disease and SNCA makers
s2k

Statistics for 2 by K table
whscore

Whittemore-Halpern scores for allele-sharing