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gap (version 1.1-12)

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

20,276

Version

1.1-12

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

August 18th, 2014

Functions in gap (1.1-12)

score statistics for testing genetic linkage of quantitative trait

genomic control based on p values

Power and sample size for case-cohort design

Bayesian false-discovery probability

Hardy-Weinberg equilibrium test using MCMC

Meta-analysis of p values

Manhattan plot with annotations

An example pedigree data

Multivariate meta-analysis based on generalized least squares

LD statistics for two multiallelic markers

Probability of familial clustering of disease

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

genomic control

Score statistics for association of traits with haplotypes

Gene counting for haplotype analysis

Haplotype reconstruction

ALDH2 markers and Alcoholism

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

multiple imputation analysis for hap

Internal functions for gap

Classic twin models

False-positive report probability

APOE/APOC1 markers and Alzheimer's

Regional association plot

A study of Parkinson's disease and MAO gene

Example data for ACEnucfam

kinship matrix for simple pedigree

Quantile-comparison plots

Gene counting for haplotype analysis

Probability of familial clustering of disease

Test/Power calculation for mediating effect

A case-control data involving four SNPs with missing genotype

Crohn's disease data

An example data for Manhattan plot with annotation

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

Genetic analysis package

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

Effect-size plot

Statistics for 2 by K table

LD statistics for two diallelic markers

Sample size calculation for mediation analysis

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

An example pedigree

AE model using nuclear family trios

Permutation tests using GENECOUNTING

print.hap.score

Print a hap.score object

Power calculation for two-stage case-control design

Preparing weight for GENECOUNTING

Gene counting for haplotype analysis

A function to prepare pedigrees in post-MAKEPED format

Chow's test for heterogeneity in two regressions

Sample size for family-based linkage and association design

Whittemore-Halpern scores for allele-sharing

Transmission/disequilibrium test of a multiallelic marker

Fixed and random effects model for meta-analysis

Plot haplotype frequencies versus haplotype score statistics

Haplotype trend regression

Converting pedigree(s) to dot file(s)

Kinship coefficient and genetic index of familiality

Example data for association plot

Heritability estimation according to twin correlations

Power for population-based association design

Bradley-Terry model for contingency table

Friedreich Ataxia data

Q-Q plot for uniformly distributed random variable

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

Cystic fibrosis data

Power for case-control association design

Obtain correlation coefficients and their variance-covariances

An example data for Manhattan plot

A utility function to read ms output

Hardy-Weinberg equlibrium test for a multiallelic marker

Functions for single nucleotide polymorphisms (SNPs)