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gap (version 1.1-1)

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

1.1-1

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

December 10th, 2010

Functions in gap (1.1-1)

Genetic analysis package

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

Gene counting for haplotype analysis

Example data for ACEnucfam

print.hap.score

Print a hap.score object

Test/Power calculation for mediating effect

Haplotype trend regression

Quantile-comparison plots

LD statistics for two diallelic markers

Permutation tests using GENECOUNTING

Sample size calculation for mediation analysis

Regional association plot

Example data for association plot

Effect-size plot

False-positive report probability

APOE/APOC1 markers and Alzheimer's

LD statistics for two multiallelic markers

Chow's test for heterogeneity in two regressions

Crohn's disease data

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

Multivariate meta-analysis based on generalized least squares

Manhattan plot of p values

Gene counting for haplotype analysis

Whittemore-Halpern scores for allele-sharing

A case-control data involving four SNPs with missing genotype

Gene counting for haplotype analysis

score statistics for testing genetic linkage of quantitative trait

Classic twin models

Bradley-Terry model for contingency table

Internal functions for gap

Cystic fibrosis data

A study of Parkinson's disease and MAO gene

Bayesian false-discovery probability

Obtain correlation coefficients and their variance-covariances

Power for case-control association design

Haplotype reconstruction

Functions for single nucleotide polymorphisms (SNPs)

Fixed and random effects model for meta-analysis

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

Kinship coefficient and genetic index of familiality

Heritability estimation according to twin correlations

genomic control

Plot haplotype frequencies versus haplotype score statistics

kinship matrix for simple pedigree

A utility function to read ms output

A study of Parkinson's disease and SNCA makers

Sample size for family-based linkage and association design

An example data for Manhattan plot

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

Score statistics for association of traits with haplotypes

A function to prepare pedigrees in post-MAKEPED format

Power and sample size for case-cohort design

Hardy-Weinberg equilibrium test using MCMC

Friedreich Ataxia data

An example data for Manhattan plot with annotation

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

Meta-analysis of p values

Hardy-Weinberg equlibrium test for a multiallelic marker

Power for population-based association design

genomic control based on p values

multiple imputation analysis for hap

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

An example pedigree

Probability of familial clustering of disease

ALDH2 markers and Alcoholism

Transmission/disequilibrium test of a multiallelic marker

Statistics for 2 by K table

An example pedigree data

Converting pedigree(s) to dot file(s)

Manhattan plot with annotations

Probability of familial clustering of disease

Q-Q plot for uniformly distributed random variable

Power calculation for two-stage case-control design

Preparing weight for GENECOUNTING

AE model using nuclear family trios

A pedigree data on 282 animals deriving from two generations

Mixed modeling with genetic relationship matrices