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gap (version 1.1-20)

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, 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.

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Version

Install

install.packages('gap')

Monthly Downloads

13,389

Version

1.1-20

License

GPL (>= 2)

Maintainer

Last Published

November 25th, 2017

Functions in gap (1.1-20)

Mixed modeling with genetic relationship matrices

A study of Parkinson's disease and APOE, LRRK2, SNCA makers

AE model using nuclear family trios

LD statistics for two diallelic markers

Bayesian false-discovery probability

Test/Power calculation for mediating effect

Power and sample size for case-cohort design

LD statistics for two multiallelic markers

score statistics for testing genetic linkage of quantitative trait

Effect-size plot

Crohn's disease data

Regional association plot

False-positive report probability

Cystic fibrosis data

Functions for single nucleotide polymorphisms (SNPs)

APOE/APOC1 markers and Alzheimer's

ALDH2 markers and Alcoholism

genomic control

Permutation tests using GENECOUNTING

Chow's test for heterogeneity in two regressions

A case-control data involving four SNPs with missing genotype

Obtain correlation coefficients and their variance-covariances

Friedreich Ataxia data

Bradley-Terry model for contingency table

Internal functions for gap

Gene counting for haplotype analysis

Sample size for family-based linkage and association design

genomic control based on p values

Haplotype reconstruction

Score statistics for association of traits with haplotypes

Gene counting for haplotype analysis

Genetic analysis package

Gene counting for haplotype analysis

Kinship coefficient and genetic index of familiality

Haplotype trend regression

Heritability estimation according to twin correlations

Hardy-Weinberg equlibrium test for a multiallelic marker

An example pedigree data

Sample size calculation for mediation analysis

An example pedigree

Meta-analysis of p values

Q-Q plot for uniformly distributed random variable

A utility function to read ms output

Manhattan plot with annotations

A function to prepare pedigrees in post-MAKEPED format

multiple imputation analysis for hap

A study of Parkinson's disease and MAO gene

Transmission/disequilibrium test of a multiallelic marker

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

Multivariate meta-analysis based on generalized least squares

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

print.hap.score

Print a hap.score object

Power for case-control association design

Quantile-comparison plots

Converting pedigree(s) to dot file(s)

Whittemore-Halpern scores for allele-sharing

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

Fixed and random effects model for meta-analysis

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

Power for population-based association design

A pedigree data on 282 animals deriving from two generations

Preparing weight for GENECOUNTING

Example data for ACEnucfam

Plot haplotype frequencies versus haplotype score statistics

Statistics for 2 by K table

Probability of familial clustering of disease

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

Probability of familial clustering of disease

Hardy-Weinberg equilibrium test using MCMC

Power calculation for two-stage case-control design

kinship matrix for simple pedigree