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gap (version 1.14)

Genetic Analysis Package

Description

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. ], 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, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

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Install

install.packages('gap')

Monthly Downloads

20,276

Version

1.14

License

GPL (>= 2)

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Repository

https://github.com/jinghuazhao/R

Maintainer

Jing Zhao

Last Published

February 19th, 2026

Functions in gap (1.14)

Bradley-Terry model for contingency table

A function to write GRM binary file

A function to write GRM file

cis.vs.trans.classification

A cis/trans classifier

genomewide plot of CNVs

Power and sample size for case-cohort design

genomic control

Estimation of the genomic control inflation statistic (lambda)

Chow's test for heterogeneity in two regressions

Two-dimensional grid

Heritability estimation based on genomic relationship matrix using JAGS

Genotype recoding

Gene counting for haplotype analysis

Genetic analysis package

LD statistics for two multiallelic markers

Mixed modeling with genetic relationship matrices

Gene counting for haplotype analysis

circos plot of CNVs.

circos.cis.vs.trans.plot

circos plot of cis/trans classification

Sample size for family-based linkage and association design

Controls for highlights

Chromosomal lengths for build 38

SNP id by chr:pos+a1/a2

Allele-to-genotype conversion

Effect size and standard error from confidence interval

Test/Power calculation for mediating effect

circos.mhtplot2

Another circos Manhattan plot

circos Manhattan plot with gene annotation

AE model using nuclear family trios

Get sd(y) from AF, n, b, se

genomic control based on p values

Bayesian false-discovery probability

score statistics for testing genetic linkage of quantitative trait

Hardy-Weinberg equilibrium test using MCMC

Permutation tests using GENECOUNTING

A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies

Kinship coefficient and genetic index of familiality

Haplotype reconstruction

Haplotype trend regression

Control for haplotype reconstruction

A function to prepare pedigrees in post-MAKEPED format

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

inv_chr_pos_a1_a2

Retrieval of chr:pos+a1/a2 according to SNP id

Controls for mhtplot

Heritability under the liability threshold model

Fixed and random effects model for meta-analysis

kinship matrix for simple pedigree

Conversion of a genotype identifier to alleles

Heritability estimation according to twin correlations

Meta-analysis of p values

Haplotype frequency estimation based on a genotype table of two multiallelic markers

Heritability and its variance

A function to read GRM binary files

Get pve and its standard error from n, z

Get b and se from AF, n, and z

Functions for single nucleotide polymorphisms

Gene counting for haplotype analysis

Mendelian randomization analysis

Mendelian Randomization forest plot

Hardy-Weinberg equlibrium test for a multiallelic marker

Transmission/disequilibrium test of a multiallelic marker

Sample size calculation for mediation analysis

Conversion of chrosome name from strings

Inverse normal transformation

Score statistics for association of traits with haplotypes

Preparing weight for GENECOUNTING

Probability of familial clustering of disease

Multiple imputation analysis for hap

P value for a normal deviate

Q-Q plot for uniformly distributed random variable

pedtodot_verbatim

Pedigree-drawing with graphviz

Probability of familial clustering of disease

log10(p) for a P value including its scientific format

Chromosomal lengths for build 37

Heritability and its variance when there is an environment component

Chromosomal lengths for build 36

log(p) for a normal deviate z

Quantile-comparison plots

A utility to generate SNPTEST sample file

Sentinel identification from GWAS summary statistics

Multivariate meta-analysis based on generalized least squares

Power for population-based association design

Conversion of chromosome names to strings

Statistics for 2 by K table

Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model

Power for case-control association design

Converting pedigree(s) to dot file(s)

A utility function to read ms output

Allele on the reverse strand

log10(p) for a normal deviate z

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

Whittemore-Halpern scores for allele-sharing

Power calculation for two-stage case-control design

A QTL cis/trans classifier

Distance-based signal identification

Annotate Manhattan or Miami Plot

Plot haplotype frequencies versus haplotype score statistics

print.hap.score

Print a hap.score object

Truncated Manhattan plot

Manhattan plot with annotations

METAL_forestplot

forest plot as R/meta's forest for METAL outputs

Disease prevalences in cases and controls

A function to read GRM file

Allele recoding

False-positive report probability

Effect-size plot

Regional association plot

LD statistics for two diallelic markers

Obtain correlation coefficients and their variance-covariances