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gap (version 0.8-2)

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, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis. In the future it will incorporate programs for path and segregation analyses, as well as other statistics in linkage and association analyses.

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Version

Install

install.packages('gap')

Monthly Downloads

20,276

Version

0.8-2

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 hua Zhao

Last Published

February 6th, 2026

Functions in gap (0.8-2)

bt

Bradley-Terry model for contingency table
s2k

Statistics for 2 by K table
kbyl

LD statistics for two multiallelic loci
gif

Kinship coefficient and genetic index of familiality
hap.em

Gene counting for haplotype analysis
hap.score

Score Statistics for Association of Traits with Haplotypes
genecounting

Gene counting for haplotype analysis
tbyt

LD statistics for two SNPs
aldh2

ALDH2 markers and Alcoholism
muvar

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

A function to prepare pedigrees in post-MAKEPED format
hla

HLA markers and Schizophrenia
pbsize

Power for population-based association design
pgc

Preparing weight for GENECOUNTING
mtdt

Transmission/disequilibrium test of a multiallelic marker
kin.morgan

kinship matrix for simple pedigree
pfc.sim

Probability of familial clustering of disease
pfc

Probability of familial clustering of disease
gcontrol

genomic control
fbsize

Sample size for family-based linkage and association design
hap

Haplotype reconstruction
hwe

Hardy-Weinberg equlibrium test
apoeapoc

APOE/APOC1 markers and Schizophrenia
mia

multiple imputation analysis for hap
whscore

Whittemore-Halpern scores for allele-sharing
fsnps

A case-control data involving four SNPs with missing genotype
gc.em

Gene counting for haplotype analysis
chow.test

Chow's test for heterogeneity in two regressions
htr

Haplotype trend regression
hwe.hardy

Hardy-Weinberg equlibrium test using MCMC
print.hap.score

Print a hap.score object
plot.hap.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
gcp

Permutation tests using GENECOUNTING
gap-internal

internal functions for gap