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gap (version 1.1-6)

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, 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

17,389

Version

1.1-6

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

March 15th, 2012

Functions in gap (1.1-6)

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

Hardy-Weinberg equlibrium test for a multiallelic marker

Power for population-based association design

Power for case-control association design

False-positive report probability

Obtain correlation coefficients and their variance-covariances

Regional association plot

Crohn's disease data

Gene counting for haplotype analysis

Power and sample size for case-cohort design

score statistics for testing genetic linkage of quantitative trait

An example pedigree

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

Meta-analysis of p values

Functions for single nucleotide polymorphisms (SNPs)

Permutation tests using GENECOUNTING

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

A study of Parkinson's disease and MAO gene

Haplotype reconstruction

An example data for Manhattan plot

Score statistics for association of traits with haplotypes

Plot haplotype frequencies versus haplotype score statistics

Sample size calculation for mediation analysis

Test/Power calculation for mediating effect

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

Q-Q plot for uniformly distributed random variable

Hardy-Weinberg equilibrium test using MCMC

Heritability estimation according to twin correlations

Whittemore-Halpern scores for allele-sharing

Bradley-Terry model for contingency table

Classic twin models

genomic control

Transmission/disequilibrium test of a multiallelic marker

Power calculation for two-stage case-control design

LD statistics for two diallelic markers

APOE/APOC1 markers and Alzheimer's

Cystic fibrosis data

Gene counting for haplotype analysis

Probability of familial clustering of disease

Multivariate meta-analysis based on generalized least squares

Genetic analysis package

Gene counting for haplotype analysis

Probability of familial clustering of disease

genomic control based on p values

multiple imputation analysis for hap

A function to prepare pedigrees in post-MAKEPED format

Example data for association plot

Effect-size plot

Bayesian false-discovery probability

Sample size for family-based linkage and association design

Internal functions for gap

Haplotype trend regression

Manhattan plot of p values

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

Statistics for 2 by K table

A case-control data involving four SNPs with missing genotype

print.hap.score

Print a hap.score object

Fixed and random effects model for meta-analysis

Preparing weight for GENECOUNTING

ALDH2 markers and Alcoholism

LD statistics for two multiallelic markers

Friedreich Ataxia data

Kinship coefficient and genetic index of familiality

kinship matrix for simple pedigree

A utility function to read ms output

Chow's test for heterogeneity in two regressions

Converting pedigree(s) to dot file(s)

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

Quantile-comparison plots