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gap (version 1.1-14)

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

1.1-14

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

June 4th, 2015

Functions in gap (1.1-14)

A pedigree data on 282 animals deriving from two generations

Score statistics for association of traits with haplotypes

A study of Parkinson's disease and MAO gene

Bradley-Terry model for contingency table

Test/Power calculation for mediating effect

Effect-size plot

Genetic analysis package

Kinship coefficient and genetic index of familiality

An example data for Manhattan plot with annotation

An example pedigree data

multiple imputation analysis for hap

AE model using nuclear family trios

Probability of familial clustering of disease

A function to prepare pedigrees in post-MAKEPED format

kinship matrix for simple pedigree

Quantile-comparison plots

Fixed and random effects model for meta-analysis

Power for population-based association design

Haplotype trend regression

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

Chow's test for heterogeneity in two regressions

Bayesian false-discovery probability

A case-control data involving four SNPs with missing genotype

ALDH2 markers and Alcoholism

Manhattan plot with annotations

Heritability estimation according to twin correlations

score statistics for testing genetic linkage of quantitative trait

Regional association plot

Mixed modeling with genetic relationship matrices

Power for case-control association design

Cystic fibrosis data

Hardy-Weinberg equlibrium test for a multiallelic marker

Example data for association plot

Functions for single nucleotide polymorphisms (SNPs)

genomic control based on p values

Q-Q plot for uniformly distributed random variable

False-positive report probability

Whittemore-Halpern scores for allele-sharing

Haplotype reconstruction

An example pedigree

Internal functions for gap

Obtain correlation coefficients and their variance-covariances

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

LD statistics for two diallelic markers

Plot haplotype frequencies versus haplotype score statistics

Converting pedigree(s) to dot file(s)

A utility function to read ms output

Transmission/disequilibrium test of a multiallelic marker

An example data for Manhattan plot

Meta-analysis of p values

print.hap.score

Print a hap.score object

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

Sample size calculation for mediation analysis

Sample size for family-based linkage and association design

Gene counting for haplotype analysis

Gene counting for haplotype analysis

Hardy-Weinberg equilibrium test using MCMC

Power calculation for two-stage case-control design

LD statistics for two multiallelic markers

Friedreich Ataxia data

Gene counting for haplotype analysis

Probability of familial clustering of disease

genomic control

Power and sample size for case-cohort design

Permutation tests using GENECOUNTING

Preparing weight for GENECOUNTING

Example data for ACEnucfam

Multivariate meta-analysis based on generalized least squares

APOE/APOC1 markers and Alzheimer's

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

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

Crohn's disease data

Classic twin models

Statistics for 2 by K table

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