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gap (version 1.1-16)

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, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates.

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Version

Install

install.packages('gap')

Monthly Downloads

16,595

Version

1.1-16

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

June 6th, 2015

Functions in gap (1.1-16)

Functions for single nucleotide polymorphisms (SNPs)

Power and sample size for case-cohort design

Probability of familial clustering of disease

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

Haplotype trend regression

ALDH2 markers and Alcoholism

Sample size for family-based linkage and association design

Score statistics for association of traits with haplotypes

Sample size calculation for mediation analysis

An example data for Manhattan plot

Power for population-based association design

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

A pedigree data on 282 animals deriving from two generations

Chow's test for heterogeneity in two regressions

An example data for Manhattan plot with annotation

Hardy-Weinberg equilibrium test using MCMC

kinship matrix for simple pedigree

Fixed and random effects model for meta-analysis

Converting pedigree(s) to dot file(s)

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

Power for case-control association design

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

Mixed modeling with genetic relationship matrices

score statistics for testing genetic linkage of quantitative trait

Bradley-Terry model for contingency table

A function to prepare pedigrees in post-MAKEPED format

Gene counting for haplotype analysis

Statistics for 2 by K table

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

LD statistics for two multiallelic markers

Kinship coefficient and genetic index of familiality

Hardy-Weinberg equlibrium test for a multiallelic marker

An example pedigree data

Haplotype reconstruction

Manhattan plot with annotations

Classic twin models

A utility function to read ms output

LD statistics for two diallelic markers

Regional association plot

Crohn's disease data

Friedreich Ataxia data

genomic control based on p values

Meta-analysis of p values

Transmission/disequilibrium test of a multiallelic marker

Q-Q plot for uniformly distributed random variable

Plot haplotype frequencies versus haplotype score statistics

Whittemore-Halpern scores for allele-sharing

A case-control data involving four SNPs with missing genotype

Genetic analysis package

Heritability estimation according to twin correlations

Example data for ACEnucfam

Permutation tests using GENECOUNTING

Effect-size plot

Internal functions for gap

Probability of familial clustering of disease

print.hap.score

Print a hap.score object

Gene counting for haplotype analysis

Example data for association plot

Obtain correlation coefficients and their variance-covariances

Gene counting for haplotype analysis

Cystic fibrosis data

Test/Power calculation for mediating effect

A study of Parkinson's disease and MAO gene

Multivariate meta-analysis based on generalized least squares

Preparing weight for GENECOUNTING

Power calculation for two-stage case-control design

genomic control

An example pedigree

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

Bayesian false-discovery probability

AE model using nuclear family trios

False-positive report probability

multiple imputation analysis for hap

APOE/APOC1 markers and Alzheimer's

Quantile-comparison plots