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gap (version 1.1-0)

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, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

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Version

Install

install.packages('gap')

Monthly Downloads

20,276

Version

1.1-0

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

November 17th, 2010

Functions in gap (1.1-0)

Friedreich Ataxia data

Fixed and random effects model for meta-analysis

Hardy-Weinberg equlibrium test for a multiallelic marker

Test/Power calculation for mediating effect

kinship matrix for simple pedigree

Bayesian false-discovery probability

LD statistics for two multiallelic markers

Regional association plot

Hardy-Weinberg equilibrium test using MCMC

Power for population-based association design

Chow's test for heterogeneity in two regressions

LD statistics for two diallelic markers

Transmission/disequilibrium test of a multiallelic marker

A function to prepare pedigrees in post-MAKEPED format

A study of Parkinson's disease and SNCA makers

Cystic fibrosis data

Preparing weight for GENECOUNTING

score statistics for testing genetic linkage of quantitative trait

Power and sample size for case-cohort design

multiple imputation analysis for hap

ALDH2 markers and Alcoholism

genomic control based on p values

Power calculation for two-stage case-control design

False-positive report probability

Obtain correlation coefficients and their variance-covariances

Gene counting for haplotype analysis

Classic twin models

Internal functions for gap

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

A case-control data involving four SNPs with missing genotype

Heritability estimation according to twin correlations

Crohn's disease data

Manhattan plot of p values

Bradley-Terry model for contingency table

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

Haplotype reconstruction

Gene counting for haplotype analysis

Probability of familial clustering of disease

Quantile-comparison plots

APOE/APOC1 markers and Alzheimer's

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

Sample size calculation for mediation analysis

genomic control

Sample size for family-based linkage and association design

Power for case-control association design

Probability of familial clustering of disease

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

Meta-analysis of p values

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

Score statistics for association of traits with haplotypes

print.hap.score

Print a hap.score object

Genetic analysis package

Plot haplotype frequencies versus haplotype score statistics

A utility function to read ms output

A study of Parkinson's disease and MAO gene

An example data for Manhattan plot

Permutation tests using GENECOUNTING

Statistics for 2 by K table

Example data for association plot

Functions for single nucleotide polymorphisms (SNPs)

Effect-size plot

Kinship coefficient and genetic index of familiality

Q-Q plot for uniformly distributed random variable

Multivariate meta-analysis based on generalized least squares

Gene counting for haplotype analysis

Converting pedigree(s) to dot file(s)

Haplotype trend regression

Whittemore-Halpern scores for allele-sharing