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gap (version 1.1-22)

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

15,115

Version

1.1-22

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

June 8th, 2018

Functions in gap (1.1-22)

Internal functions for gap

Haplotype reconstruction

Sample size for family-based linkage and association design

Permutation tests using GENECOUNTING

Gene counting for haplotype analysis

An example pedigree

Transmission/disequilibrium test of a multiallelic marker

Haplotype trend regression

An example pedigree data

Regional association plot

LD statistics for two multiallelic markers

score statistics for testing genetic linkage of quantitative trait

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

Gene counting for haplotype analysis

Hardy-Weinberg equlibrium test for a multiallelic marker

Obtain correlation coefficients and their variance-covariances

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

Preparing weight for GENECOUNTING

Gene counting for haplotype analysis

Hardy-Weinberg equilibrium test using MCMC

Crohn's disease data

A function to prepare pedigrees in post-MAKEPED format

Fixed and random effects model for meta-analysis

Kinship coefficient and genetic index of familiality

Manhattan plot with annotations

A study of Parkinson's disease and MAO gene

Heritability estimation according to twin correlations

kinship matrix for simple pedigree

genomic control

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

genomic control based on p values

Sample size calculation for mediation analysis

Score statistics for association of traits with haplotypes

Plot haplotype frequencies versus haplotype score statistics

Meta-analysis of p values

A pedigree data on 282 animals deriving from two generations

Statistics for 2 by K table

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

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

multiple imputation analysis for hap

Power for case-control association design

Example data for ACEnucfam

print.hap.score

Print a hap.score object

Q-Q plot for uniformly distributed random variable

Quantile-comparison plots

Whittemore-Halpern scores for allele-sharing

Power for population-based association design

Multivariate meta-analysis based on generalized least squares

Converting pedigree(s) to dot file(s)

A utility function to read ms output

Power calculation for two-stage case-control design

Probability of familial clustering of disease

Probability of familial clustering of disease

Functions for single nucleotide polymorphisms (SNPs)

Effect-size plot

Mixed modeling with genetic relationship matrices

LD statistics for two diallelic markers

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

Test/Power calculation for mediating effect

AE model using nuclear family trios

False-positive report probability

Bayesian false-discovery probability

Chow's test for heterogeneity in two regressions

Cystic fibrosis data

APOE/APOC1 markers and Alzheimer's

ALDH2 markers and Alcoholism

A case-control data involving four SNPs with missing genotype

Power and sample size for case-cohort design

Bradley-Terry model for contingency table

Friedreich Ataxia data

Genetic analysis package