Learn R Programming

⚠️There's a newer version (1.6) of this package.Take me there.

gap (version 1.1-17)

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.

Copy Link

Version

Install

install.packages('gap')

Monthly Downloads

15,115

Version

1.1-17

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

April 19th, 2017

Functions in gap (1.1-17)

Example data for association plot

Effect-size plot

AE model using nuclear family trios

Bayesian false-discovery probability

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

Functions for single nucleotide polymorphisms (SNPs)

False-positive report probability

LD statistics for two diallelic markers

LD statistics for two multiallelic markers

Mixed modeling with genetic relationship matrices

Obtain correlation coefficients and their variance-covariances

Bradley-Terry model for contingency table

Power and sample size for case-cohort design

Cystic fibrosis data

Gene counting for haplotype analysis

genomic control

APOE/APOC1 markers and Alzheimer's

Regional association plot

Sample size for family-based linkage and association design

Internal functions for gap

Genetic analysis package

Haplotype trend regression

An example data for Manhattan plot with annotation

kinship matrix for simple pedigree

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

Chow's test for heterogeneity in two regressions

score statistics for testing genetic linkage of quantitative trait

Permutation tests using GENECOUNTING

Example data for ACEnucfam

An example data for Manhattan plot

Power for population-based association design

genomic control based on p values

Test/Power calculation for mediating effect

ALDH2 markers and Alcoholism

Crohn's disease data

Heritability estimation according to twin correlations

Haplotype reconstruction

An example pedigree data

An example pedigree

Hardy-Weinberg equlibrium test for a multiallelic marker

Gene counting for haplotype analysis

Kinship coefficient and genetic index of familiality

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

Hardy-Weinberg equilibrium test using MCMC

Probability of familial clustering of disease

Preparing weight for GENECOUNTING

Manhattan plot with annotations

Friedreich Ataxia data

Gene counting for haplotype analysis

Score statistics for association of traits with haplotypes

Sample size calculation for mediation analysis

multiple imputation analysis for hap

Transmission/disequilibrium test of a multiallelic marker

Meta-analysis of p values

Fixed and random effects model for meta-analysis

A pedigree data on 282 animals deriving from two generations

Plot haplotype frequencies versus haplotype score statistics

print.hap.score

Print a hap.score object

Multivariate meta-analysis based on generalized least squares

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

A utility function to read ms output

Power for case-control association design

A case-control data involving four SNPs with missing genotype

A function to prepare pedigrees in post-MAKEPED format

A study of Parkinson's disease and MAO gene

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

Converting pedigree(s) to dot file(s)

Probability of familial clustering of disease

Power calculation for two-stage case-control design

Whittemore-Halpern scores for allele-sharing

Statistics for 2 by K table

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

Quantile-comparison plots

Q-Q plot for uniformly distributed random variable