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gap (version 1.0-15)

Genetic analysis package

Description

It is designed as 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 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

1.0-15

License

GPL (>=2)

Maintainer

Jing Zhao

Last Published

February 6th, 2026

Functions in gap (1.0-15)

bt

Bradley-Terry model for contingency table
LDkl

LD statistics for two multiallelic markers
CDKN

Example data for association plot
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
comp.score

score statistics for testing genetic linkage of quantitative trait
mao

A study of Parkinson's disease and MAO gene
genecounting

Gene counting for haplotype analysis
fa

Friedreich Ataxia data
kin.morgan

kinship matrix for simple pedigree
hla

The HLA data
asplot

Regional association plot
htr

Haplotype trend regression
SNP

Functions for single nucleotide polymorphisms (SNPs)
hap.em

Gene counting for haplotype analysis
print.hap.score

Print a hap.score object
apoeapoc

APOE/APOC1 markers and schizophrenia
hap

Haplotype reconstruction
chow.test

Chow's test for heterogeneity in two regressions
crohn

Crohn's disease data
BFDP

Bayesian false-discovery probability
cf

Cystic fibrosis data
gap-package

Genetic analysis package
mia

multiple imputation analysis for hap
hwe

Hardy-Weinberg equlibrium test for a multiallelic marker
makeped

A function to prepare pedigrees in post-MAKEPED format
nep499

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

Quantile-comparison plots
plot.hap.score

Plot haplotype frequencies versus haplotype score statistics
aldh2

ALDH2 markers and Alcoholism
fsnps

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

Effect-size plot
twinan90

Classic twin models
qqunif

Q-Q plot for uniformly distributed random variable
fbsize

Sample size for family-based linkage and association design
metareg

Fixed and random effects model for meta-analysis
s2k

Statistics for 2 by K table
gcp

Permutation tests using GENECOUNTING
tscc

Power calculation for two-stage case-control design
muvar

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

Transmission/disequilibrium test of a multiallelic marker
metap

Meta-analysis of p values
LD22

LD statistics for two diallelic markers
gcontrol

genomic control
whscore

Whittemore-Halpern scores for allele-sharing
pgc

Preparing weight for GENECOUNTING
gc.em

Gene counting for haplotype analysis
pfc.sim

Probability of familial clustering of disease
pbsize2

Power for case-control association design
gif

Kinship coefficient and genetic index of familiality
pfc

Probability of familial clustering of disease
ccsize

Power and sample size for case-cohort design
hap.score

Score statistics for association of traits with haplotypes
gap-internal

internal functions for gap
pbsize

Power for population-based association design
mhtplot

Manhattan plot of p values
FPRP

False-positive report probability
snca

A study of Parkinson's disease and SNCA makers
gcontrol2

genomic control based on p values
pedtodot

Converting pedigree(s) to dot file(s)