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gap (version 1.0-13)

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

1.0-13

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 (1.0-13)

apoeapoc

APOE/APOC1 markers and Schizophrenia
kin.morgan

kinship matrix for simple pedigree
qqunif

Q-Q plot for uniformly distributed random variable
gif

Kinship coefficient and genetic index of familiality
fsnps

A case-control data involving four SNPs with missing genotype
nep499

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

LD statistics for two SNPs
makeped

A function to prepare pedigrees in post-MAKEPED format
hap.em

Gene counting for haplotype analysis
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
ccsize

Power and sample size for case-cohort design
hla

The HLA data
genecounting

Gene counting for haplotype analysis
plot.hap.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
mia

multiple imputation analysis for hap
fa

Friedreich Ataxia data
pedtodot

Converting pedigree(s) to dot file(s)
gc.em

Gene counting for haplotype analysis
hwe

Hardy-Weinberg equlibrium test for multiallelic marker
twinan90

Classic twin models
pfc

Probability of familial clustering of disease
tscc

Power calculation for two-stage case-control design
gap-internal

internal functions for gap
mao

A study of Parkinson's disease and MAO gene
print.hap.score

Print a hap.score object
crohn

Crohn disease data
kbyl

LD statistics for two multiallelic loci
hap.score

Score statistics for association of traits with haplotypes
mtdt

Transmission/disequilibrium test of a multiallelic marker
aldh2

ALDH2 markers and Alcoholism
gcp

Permutation tests using GENECOUNTING
s2k

Statistics for 2 by K table
FPRP

False-positive report probability
gcontrol

genomic control
comp.score

score statistics for testing genetic linkage of quantitative trait
bt

Bradley-Terry model for contingency table
whscore

Whittemore-Halpern scores for allele-sharing
gap-package

Genetic analysis package
chow.test

Chow's test for heterogeneity in two regressions
hap

Haplotype reconstruction
muvar

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

Probability of familial clustering of disease
fbsize

Sample size for family-based linkage and association design
pgc

Preparing weight for GENECOUNTING
BFDP

Bayesian false-discovery probability
pbsize

Power for population-based association design
snca

A study of Parkinson's disease and SNCA makers
htr

Haplotype trend regression
cf

Cystic Fibrosis data