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gap (version 1.1-21)

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

1.1-21

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

January 24th, 2018

Functions in gap (1.1-21)

Mixed modeling with genetic relationship matrices

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

Functions for single nucleotide polymorphisms (SNPs)

Test/Power calculation for mediating effect

LD statistics for two diallelic markers

LD statistics for two multiallelic markers

Effect-size plot

AE model using nuclear family trios

Bayesian false-discovery probability

Regional association plot

Obtain correlation coefficients and their variance-covariances

Friedreich Ataxia data

Sample size for family-based linkage and association design

score statistics for testing genetic linkage of quantitative trait

Crohn's disease data

genomic control

False-positive report probability

A case-control data involving four SNPs with missing genotype

Internal functions for gap

Score statistics for association of traits with haplotypes

Cystic fibrosis data

Chow's test for heterogeneity in two regressions

Permutation tests using GENECOUNTING

Gene counting for haplotype analysis

Haplotype trend regression

Bradley-Terry model for contingency table

Power and sample size for case-cohort design

Haplotype reconstruction

genomic control based on p values

Kinship coefficient and genetic index of familiality

Heritability estimation according to twin correlations

An example pedigree data

An example pedigree

ALDH2 markers and Alcoholism

APOE/APOC1 markers and Alzheimer's

Genetic analysis package

kinship matrix for simple pedigree

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

Manhattan plot with annotations

multiple imputation analysis for hap

Preparing weight for GENECOUNTING

Plot haplotype frequencies versus haplotype score statistics

Gene counting for haplotype analysis

A function to prepare pedigrees in post-MAKEPED format

A study of Parkinson's disease and MAO gene

Power for case-control association design

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

Hardy-Weinberg equilibrium test using MCMC

Fixed and random effects model for meta-analysis

Gene counting for haplotype analysis

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

Power for population-based association design

print.hap.score

Print a hap.score object

Hardy-Weinberg equlibrium test for a multiallelic marker

Sample size calculation for mediation analysis

Meta-analysis of p values

A pedigree data on 282 animals deriving from two generations

Transmission/disequilibrium test of a multiallelic marker

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

Example data for ACEnucfam

Q-Q plot for uniformly distributed random variable

A utility function to read ms output

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

Multivariate meta-analysis based on generalized least squares

Probability of familial clustering of disease

Converting pedigree(s) to dot file(s)

Statistics for 2 by K table

Power calculation for two-stage case-control design

Probability of familial clustering of disease

Quantile-comparison plots

Whittemore-Halpern scores for allele-sharing