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gap (version 1.1-3)

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

15,115

Version

1.1-3

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

December 6th, 2011

Functions in gap (1.1-3)

Regional association plot

APOE/APOC1 markers and Alzheimer's

Sample size for family-based linkage and association design

genomic control

Hardy-Weinberg equlibrium test for a multiallelic marker

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

Effect-size plot

Genetic analysis package

LD statistics for two multiallelic markers

A case-control data involving four SNPs with missing genotype

Score statistics for association of traits with haplotypes

Test/Power calculation for mediating effect

Cystic fibrosis data

Haplotype reconstruction

Gene counting for haplotype analysis

An example pedigree

Meta-analysis of p values

Statistics for 2 by K table

Power for population-based association design

A utility function to read ms output

Probability of familial clustering of disease

Q-Q plot for uniformly distributed random variable

Whittemore-Halpern scores for allele-sharing

Power for case-control association design

Transmission/disequilibrium test of a multiallelic marker

Obtain correlation coefficients and their variance-covariances

Functions for single nucleotide polymorphisms (SNPs)

Gene counting for haplotype analysis

Sample size calculation for mediation analysis

Kinship coefficient and genetic index of familiality

score statistics for testing genetic linkage of quantitative trait

An example data for Manhattan plot

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

Preparing weight for GENECOUNTING

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

Haplotype trend regression

Multivariate meta-analysis based on generalized least squares

Example data for association plot

kinship matrix for simple pedigree

Permutation tests using GENECOUNTING

Manhattan plot of p values

Power and sample size for case-cohort design

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

Heritability estimation according to twin correlations

Gene counting for haplotype analysis

Probability of familial clustering of disease

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

Plot haplotype frequencies versus haplotype score statistics

Internal functions for gap

Classic twin models

Hardy-Weinberg equilibrium test using MCMC

Quantile-comparison plots

print.hap.score

Print a hap.score object

LD statistics for two diallelic markers

Bayesian false-discovery probability

Bradley-Terry model for contingency table

Chow's test for heterogeneity in two regressions

ALDH2 markers and Alcoholism

multiple imputation analysis for hap

genomic control based on p values

Power calculation for two-stage case-control design

False-positive report probability

Friedreich Ataxia data

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

A study of Parkinson's disease and MAO gene

Crohn's disease data

Fixed and random effects model for meta-analysis

Converting pedigree(s) to dot file(s)

A function to prepare pedigrees in post-MAKEPED format