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gap (version 1.0-12)

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

1.0-12

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 (1.0-12)

fa

Friedreich Ataxia data
ccsize

Power and sample size for case-cohort design
FPRP

False-positive report probability
gcp

Permutation tests using GENECOUNTING
apoeapoc

APOE/APOC1 markers and Schizophrenia
gc.em

Gene counting for haplotype analysis
hla

The HLA data
fsnps

A case-control data involving four SNPs with missing genotype
chow.test

Chow's test for heterogeneity in two regressions
gap-internal

internal functions for gap
BFDP

Bayesian false-discovery probability
comp.score

score statistics for testing genetic linkage of quantitative trait
fbsize

Sample size for family-based linkage and association design
aldh2

ALDH2 markers and Alcoholism
gcontrol

genomic control
hwe

Hardy-Weinberg equlibrium test for multiallelic marker
cf

Cystic Fibrosis data
hap.em

Gene counting for haplotype analysis
pfc.sim

Probability of familial clustering of disease
hap

Haplotype reconstruction
crohn

Crohn disease data
nep499

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

A function to prepare pedigrees in post-MAKEPED format
pgc

Preparing weight for GENECOUNTING
hap.score

Score statistics for association of traits with haplotypes
muvar

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

LD statistics for two SNPs
mtdt

Transmission/disequilibrium test of a multiallelic marker
qqunif

Q-Q plot for uniformly distributed random variable
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
gif

Kinship coefficient and genetic index of familiality
pbsize

Power for population-based association design
plot.hap.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
pedtodot

Converting pedigree(s) to dot file(s)
kbyl

LD statistics for two multiallelic loci
pfc

Probability of familial clustering of disease
mao

A study of Parkinson's disease and MAO gene
htr

Haplotype trend regression
genecounting

Gene counting for haplotype analysis
bt

Bradley-Terry model for contingency table
twinan90

Classic twin models
gap-package

Genetic analysis package
mia

multiple imputation analysis for hap
s2k

Statistics for 2 by K table
tscc

Power calculation for two-stage case-control design
whscore

Whittemore-Halpern scores for allele-sharing
print.hap.score

Print a hap.score object
snca

A study of Parkinson's disease and SNCA makers
kin.morgan

kinship matrix for simple pedigree