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gap (version 1.1-2)

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

16,595

Version

1.1-2

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

May 3rd, 2011

Functions in gap (1.1-2)

Friedreich Ataxia data

Sample size for family-based linkage and association design

Gene counting for haplotype analysis

Effect-size plot

Classic twin models

A study of Parkinson's disease and SNCA makers

Example data for association plot

Genetic analysis package

Score statistics for association of traits with haplotypes

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

Hardy-Weinberg equlibrium test for a multiallelic marker

Power calculation for two-stage case-control design

False-positive report probability

Crohn's disease data

Heritability estimation according to twin correlations

genomic control

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

Power for case-control association design

Whittemore-Halpern scores for allele-sharing

LD statistics for two multiallelic markers

Bradley-Terry model for contingency table

Meta-analysis of p values

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

An example data for Manhattan plot

Haplotype reconstruction

Q-Q plot for uniformly distributed random variable

A utility function to read ms output

Cystic fibrosis data

Power and sample size for case-cohort design

Chow's test for heterogeneity in two regressions

Gene counting for haplotype analysis

Haplotype trend regression

Sample size calculation for mediation analysis

Power for population-based association design

Multivariate meta-analysis based on generalized least squares

A case-control data involving four SNPs with missing genotype

Statistics for 2 by K table

Permutation tests using GENECOUNTING

score statistics for testing genetic linkage of quantitative trait

Fixed and random effects model for meta-analysis

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

kinship matrix for simple pedigree

genomic control based on p values

Functions for single nucleotide polymorphisms (SNPs)

A function to prepare pedigrees in post-MAKEPED format

Quantile-comparison plots

Probability of familial clustering of disease

LD statistics for two diallelic markers

APOE/APOC1 markers and Alzheimer's

Preparing weight for GENECOUNTING

An example pedigree

Probability of familial clustering of disease

Hardy-Weinberg equilibrium test using MCMC

Obtain correlation coefficients and their variance-covariances

Test/Power calculation for mediating effect

A study of Parkinson's disease and MAO gene

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

Converting pedigree(s) to dot file(s)

Transmission/disequilibrium test of a multiallelic marker

Manhattan plot of p values

Plot haplotype frequencies versus haplotype score statistics

Bayesian false-discovery probability

Internal functions for gap

Kinship coefficient and genetic index of familiality

Gene counting for haplotype analysis

ALDH2 markers and Alcoholism

Regional association plot

print.hap.score

Print a hap.score object

multiple imputation analysis for hap