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gap (version 1.0-23)

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

1.0-23

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

June 25th, 2010

Functions in gap (1.0-23)

Probability of familial clustering of disease

Effect-size plot

Regional association plot

LD statistics for two multiallelic markers

Internal functions for gap

Bradley-Terry model for contingency table

Power for case-control association design

Heritability estimation according to twin correlations

Multivariate meta-analysis based on generalized least squares

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

print.hap.score

Print a hap.score object

A case-control data involving four SNPs with missing genotype

Fixed and random effects model for meta-analysis

Plot haplotype frequencies versus haplotype score statistics

A study of Parkinson's disease and MAO gene

Test/Power calculation for mediating effect

Chow's test for heterogeneity in two regressions

Hardy-Weinberg equlibrium test for a multiallelic marker

Crohn's disease data

Sample size calculation for mediation analysis

Sample size for family-based linkage and association design

Hardy-Weinberg equilibrium test using MCMC

Kinship coefficient and genetic index of familiality

Example data for association plot

LD statistics for two diallelic markers

score statistics for testing genetic linkage of quantitative trait

genomic control

kinship matrix for simple pedigree

Converting pedigree(s) to dot file(s)

Obtain correlation coefficients and their variance-covariances

Genetic analysis package

A utility function to read ms output

Statistics for 2 by K table

False-positive report probability

Quantile-comparison plots

Classic twin models

Q-Q plot for uniformly distributed random variable

Whittemore-Halpern scores for allele-sharing

A study of Parkinson's disease and SNCA makers

Cystic fibrosis data

Probability of familial clustering of disease

Gene counting for haplotype analysis

Preparing weight for GENECOUNTING

Bayesian false-discovery probability

Power and sample size for case-cohort design

Manhattan plot of p values

Gene counting for haplotype analysis

A function to prepare pedigrees in post-MAKEPED format

Friedreich Ataxia data

Functions for single nucleotide polymorphisms (SNPs)

APOE/APOC1 markers and Alzheimer's

ALDH2 markers and Alcoholism

Power calculation for two-stage case-control design

Meta-analysis of p values

Haplotype reconstruction

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

multiple imputation analysis for hap

Permutation tests using GENECOUNTING

Power for population-based association design

Score statistics for association of traits with haplotypes

Gene counting for haplotype analysis

genomic control based on p values

Haplotype trend regression

Transmission/disequilibrium test of a multiallelic marker

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

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

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