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gap (version 1.1-8)

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

14,766

Version

1.1-8

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

February 26th, 2013

Functions in gap (1.1-8)

LD statistics for two multiallelic markers

A case-control data involving four SNPs with missing genotype

Permutation tests using GENECOUNTING

genomic control

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

Effect-size plot

Bradley-Terry model for contingency table

Haplotype reconstruction

Haplotype trend regression

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

A function to prepare pedigrees in post-MAKEPED format

Gene counting for haplotype analysis

Whittemore-Halpern scores for allele-sharing

Obtain correlation coefficients and their variance-covariances

Gene counting for haplotype analysis

Hardy-Weinberg equlibrium test for a multiallelic marker

An example pedigree

An example data for Manhattan plot

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

Plot haplotype frequencies versus haplotype score statistics

Multivariate meta-analysis based on generalized least squares

Converting pedigree(s) to dot file(s)

Probability of familial clustering of disease

False-positive report probability

Classic twin models

Crohn's disease data

A study of Parkinson's disease and MAO gene

Bayesian false-discovery probability

Functions for single nucleotide polymorphisms (SNPs)

Genetic analysis package

Internal functions for gap

APOE/APOC1 markers and Alzheimer's

Chow's test for heterogeneity in two regressions

score statistics for testing genetic linkage of quantitative trait

Power for case-control association design

print.hap.score

Print a hap.score object

ALDH2 markers and Alcoholism

Manhattan plot with annotations

Power for population-based association design

Probability of familial clustering of disease

Score statistics for association of traits with haplotypes

Example data for association plot

AE model using nuclear family trios

Friedreich Ataxia data

Test/Power calculation for mediating effect

Kinship coefficient and genetic index of familiality

Cystic fibrosis data

Heritability estimation according to twin correlations

Meta-analysis of p values

multiple imputation analysis for hap

Power and sample size for case-cohort design

Sample size for family-based linkage and association design

kinship matrix for simple pedigree

Power calculation for two-stage case-control design

An example pedigree data

Statistics for 2 by K table

Hardy-Weinberg equilibrium test using MCMC

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

Transmission/disequilibrium test of a multiallelic marker

Example data for ACEnucfam

Preparing weight for GENECOUNTING

Regional association plot

LD statistics for two diallelic markers

genomic control based on p values

Quantile-comparison plots

Q-Q plot for uniformly distributed random variable

A utility function to read ms output

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

Gene counting for haplotype analysis

An example data for Manhattan plot with annotation

Sample size calculation for mediation analysis

Fixed and random effects model for meta-analysis

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