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gap (version 1.1-13)

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

17,389

Version

1.1-13

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

June 3rd, 2015

Functions in gap (1.1-13)

Effect-size plot

APOE/APOC1 markers and Alzheimer's

Obtain correlation coefficients and their variance-covariances

Crohn's disease data

Power and sample size for case-cohort design

LD statistics for two multiallelic markers

Score statistics for association of traits with haplotypes

Chow's test for heterogeneity in two regressions

score statistics for testing genetic linkage of quantitative trait

Haplotype trend regression

Heritability estimation according to twin correlations

Gene counting for haplotype analysis

Manhattan plot with annotations

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

Probability of familial clustering of disease

A pedigree data on 282 animals deriving from two generations

kinship matrix for simple pedigree

Power for population-based association design

print.hap.score

Print a hap.score object

Quantile-comparison plots

genomic control

Preparing weight for GENECOUNTING

Bayesian false-discovery probability

Internal functions for gap

genomic control based on p values

Hardy-Weinberg equilibrium test using MCMC

Example data for ACEnucfam

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

Transmission/disequilibrium test of a multiallelic marker

Power calculation for two-stage case-control design

Classic twin models

Example data for association plot

ALDH2 markers and Alcoholism

Gene counting for haplotype analysis

Hardy-Weinberg equlibrium test for a multiallelic marker

Gene counting for haplotype analysis

Probability of familial clustering of disease

Bradley-Terry model for contingency table

Converting pedigree(s) to dot file(s)

Plot haplotype frequencies versus haplotype score statistics

Kinship coefficient and genetic index of familiality

Friedreich Ataxia data

False-positive report probability

Functions for single nucleotide polymorphisms (SNPs)

Haplotype reconstruction

A study of Parkinson's disease and MAO gene

Statistics for 2 by K table

Test/Power calculation for mediating effect

A case-control data involving four SNPs with missing genotype

An example pedigree data

Meta-analysis of p values

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

Power for case-control association design

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

An example pedigree

AE model using nuclear family trios

Sample size for family-based linkage and association design

Sample size calculation for mediation analysis

A utility function to read ms output

Whittemore-Halpern scores for allele-sharing

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

Q-Q plot for uniformly distributed random variable

LD statistics for two diallelic markers

An example data for Manhattan plot with annotation

Regional association plot

Genetic analysis package

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

Permutation tests using GENECOUNTING

An example data for Manhattan plot

Multivariate meta-analysis based on generalized least squares

Cystic fibrosis data

Fixed and random effects model for meta-analysis

multiple imputation analysis for hap

Mixed modeling with genetic relationship matrices

A function to prepare pedigrees in post-MAKEPED format