Genetic Analysis Package
A function to read GRM binary files
Allele on the reverse strand
Start shinygap
Statistics for 2 by K table
Sentinel identification from GWAS summary statistics
Functions for single nucleotide polymorphisms
A utility to generate SNPTEST sample file
Power calculation for two-stage case-control design
Whittemore-Halpern scores for allele-sharing
A function to write GRM file
A function to write GRM binary file
Conversion of chromosome names to strings
Allele-to-genotype conversion
circos Manhattan plot with gene annotation
Test/Power calculation for mediating effect
AE model using nuclear family trios
Allele recoding
Regional association plot
Obtain correlation coefficients and their variance-covariances
Bayesian false-discovery probability
Bradley-Terry model for contingency table
Power and sample size for case-cohort design
Chow's test for heterogeneity in two regressions
SNP id by chr:pos+a1/a2
Effect size and standard error from confidence interval
circos plot of cis/trans classification
circos plot of CNVs.
Heritability and its variance when there is an environment component
Another circos Manhattan plot
A cis/trans classifier
genomewide plot of CNVs
score statistics for testing genetic linkage of quantitative trait
Credible set
Effect-size plot
Heritability under the liability threshold model
Sample size for family-based linkage and association design
False-positive report probability
Conversion of a genotype identifier to alleles
Genetic analysis package
Gene counting for haplotype analysis
Estimation of the genomic control inflation statistic (lambda)
genomic control
Inverse normal transformation
Conversion of chrosome name from strings
genomic control based on p values
Permutation tests using GENECOUNTING
Gene counting for haplotype analysis
Genotype recoding
Get b and se from AF, n, and z
Get pve and its standard error from n, z
Disease prevalences in cases and controls
Get sd(y) from AF, n, b, se
Kinship coefficient and genetic index of familiality
Two-dimensional grid
Heritability estimation according to twin correlations
Heritability estimation based on genomic relationship matrix using JAG...
Heritability and its variance
Control for haplotype reconstruction
Gene counting for haplotype analysis
Haplotype reconstruction
Score statistics for association of traits with haplotypes
Controls for highlights
Haplotype trend regression
Controls for mhtplot
Manhattan plot
Truncated Manhattan plot
A likelihood ratio test of population Hardy-Weinberg equilibrium for c...
Hardy-Weinberg equilibrium test using MCMC
Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
Hardy-Weinberg equlibrium test for a multiallelic marker
Retrieval of chr:pos+a1/a2 according to SNP id
kinship matrix for simple pedigree
Haplotype frequency estimation based on a genotype table of two multia...
Annotate Manhattan or Miami Plot
LD statistics for two diallelic markers
LD statistics for two multiallelic markers
log10(p) for a normal deviate z
log10(p) for a P value including its scientific format
log(p) for a normal deviate z
Manhattan plot with annotations
A function to prepare pedigrees in post-MAKEPED format
Sample size calculation for mediation analysis
Mixed modeling with genetic relationship matrices
forest plot as R/meta's forest for METAL outputs
Meta-analysis of p values
Fixed and random effects model for meta-analysis
Multiple imputation analysis for hap
Miami plot
Miami Plot
Mendelian Randomization forest plot
Multivariate meta-analysis based on generalized least squares
Mendelian randomization analysis
Transmission/disequilibrium test of a multiallelic marker
Transmission/disequilibrium test of a multiallelic marker by Bradley-T...
Means and variances under 1- and 2- locus (biallelic) QTL model
Power for population-based association design
Power for case-control association design
Pedigree-drawing with graphviz
Converting pedigree(s) to dot file(s)
Probability of familial clustering of disease
Probability of familial clustering of disease
Preparing weight for GENECOUNTING
Plot haplotype frequencies versus haplotype score statistics
Print a hap.score object
P value for a normal deviate
Quantile-comparison plots
Q-Q plot for uniformly distributed random variable
A utility function to read ms output
2D QTL plot
2D QTL plotly
3D QTL plot
A QTL cis/trans classifier
Distance-based signal identification
A function to read GRM file
As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], 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).