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gap (version 1.9)

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

1.9

License

GPL (>= 2)

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Repository

https://github.com/jinghuazhao/R

Maintainer

Jing Zhao

Last Published

February 6th, 2026

Functions in gap (1.9)

Gene counting for haplotype analysis

Estimation of the genomic control inflation statistic (lambda)

score statistics for testing genetic linkage of quantitative trait

genomic control based on p values

Genetic analysis package

genomic control

Permutation tests using GENECOUNTING

Conversion of a genotype identifier to alleles

Sample size for family-based linkage and association design

Two-dimensional grid

Genotype recoding

Gene counting for haplotype analysis

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

Heritability estimation based on genomic relationship matrix using JAGS

Heritability and its variance

Get pve and its standard error from n, z

Get b and se from AF, n, and z

Kinship coefficient and genetic index of familiality

Heritability and its variance when there is an environment component

Controls for highlights

Control for haplotype reconstruction

Haplotype reconstruction

Heritability under the liability threshold model

Chromosomal lengths for build 37

Heritability estimation according to twin correlations

Gene counting for haplotype analysis

Chromosomal lengths for build 38

Chromosomal lengths for build 36

Hardy-Weinberg equilibrium test using MCMC

Score statistics for association of traits with haplotypes

Inverse normal transformation

kinship matrix for simple pedigree

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

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

Hardy-Weinberg equlibrium test for a multiallelic marker

Conversion of chrosome name from strings

Haplotype trend regression

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

inv_chr_pos_a1_a2

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

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

Meta-analysis of p values

Controls for mhtplot

Annotate Manhattan or Miami Plot

log10(p) for a normal deviate z

log(p) for a normal deviate z

Fixed and random effects model for meta-analysis

A function to prepare pedigrees in post-MAKEPED format

Sample size calculation for mediation analysis

Multiple imputation analysis for hap

Truncated Manhattan plot

Mendelian Randomization forest plot

Mendelian randomization analysis

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

Manhattan plot with annotations

Transmission/disequilibrium test of a multiallelic marker

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

Plot haplotype frequencies versus haplotype score statistics

Preparing weight for GENECOUNTING

Power for case-control association design

Converting pedigree(s) to dot file(s)

Multivariate meta-analysis based on generalized least squares

Power for population-based association design

pedtodot_verbatim

Pedigree-drawing with graphviz

Probability of familial clustering of disease

print.hap.score

Print a hap.score object

Probability of familial clustering of disease

Distance-based signal identification

Quantile-comparison plots

P value for a normal deviate

A QTL cis/trans classifier

Allele on the reverse strand

A utility function to read ms output

Q-Q plot for uniformly distributed random variable

Whittemore-Halpern scores for allele-sharing

Power calculation for two-stage case-control design

Sentinel identification from GWAS summary statistics

A utility to generate SNPTEST sample file

Statistics for 2 by K table

Conversion of chromosome names to strings

LD statistics for two diallelic markers

Disease prevalences in cases and controls

A function to read GRM file

Allele-to-genotype conversion

A function to read GRM binary files

A function to write GRM file

Effect-size plot

False-positive report probability

LD statistics for two multiallelic markers

Bayesian false-discovery probability

Mixed modeling with genetic relationship matrices

Functions for single nucleotide polymorphisms

SNP id by chr:pos+a1/a2

Effect size and standard error from confidence interval

Obtain correlation coefficients and their variance-covariances

METAL_forestplot

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

AE model using nuclear family trios

cis.vs.trans.classification

A cis/trans classifier

genomewide plot of CNVs

Test/Power calculation for mediating effect

Allele recoding

Regional association plot

Bradley-Terry model for contingency table

Power and sample size for case-cohort design

circos.mhtplot2

Another circos Manhattan plot

circos Manhattan plot with gene annotation

A function to write GRM binary file

circos.cis.vs.trans.plot

circos plot of cis/trans classification

circos plot of CNVs.

Chow's test for heterogeneity in two regressions