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gap (version 1.1-9)

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, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

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Version

Install

install.packages('gap')

Monthly Downloads

15,115

Version

1.1-9

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

April 8th, 2013

Functions in gap (1.1-9)

Converting pedigree(s) to dot file(s)

LD statistics for two diallelic markers

Crohn's disease data

LD statistics for two multiallelic markers

Bayesian false-discovery probability

genomic control

Haplotype trend regression

A function to prepare pedigrees in post-MAKEPED format

Functions for single nucleotide polymorphisms (SNPs)

An example data for Manhattan plot

A case-control data involving four SNPs with missing genotype

Heritability estimation according to twin correlations

Transmission/disequilibrium test of a multiallelic marker

False-positive report probability

ALDH2 markers and Alcoholism

Friedreich Ataxia data

Internal functions for gap

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

Haplotype reconstruction

An example pedigree data

Score statistics for association of traits with haplotypes

A utility function to read ms output

Permutation tests using GENECOUNTING

Sample size for family-based linkage and association design

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

Power calculation for two-stage case-control design

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

Effect-size plot

Sample size calculation for mediation analysis

Multivariate meta-analysis based on generalized least squares

Plot haplotype frequencies versus haplotype score statistics

A study of Parkinson's disease and MAO gene

Meta-analysis of p values

Kinship coefficient and genetic index of familiality

AE model using nuclear family trios

APOE/APOC1 markers and Alzheimer's

Obtain correlation coefficients and their variance-covariances

Genetic analysis package

Power and sample size for case-cohort design

Whittemore-Halpern scores for allele-sharing

Example data for association plot

genomic control based on p values

score statistics for testing genetic linkage of quantitative trait

kinship matrix for simple pedigree

Hardy-Weinberg equilibrium test using MCMC

Example data for ACEnucfam

Gene counting for haplotype analysis

Test/Power calculation for mediating effect

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

Hardy-Weinberg equlibrium test for a multiallelic marker

An example pedigree

Regional association plot

Classic twin models

Quantile-comparison plots

multiple imputation analysis for hap

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

Probability of familial clustering of disease

Gene counting for haplotype analysis

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

Chow's test for heterogeneity in two regressions

Fixed and random effects model for meta-analysis

Statistics for 2 by K table

An example data for Manhattan plot with annotation

print.hap.score

Print a hap.score object

Power for case-control association design

Bradley-Terry model for contingency table

Cystic fibrosis data

Manhattan plot with annotations

Gene counting for haplotype analysis

Preparing weight for GENECOUNTING

Probability of familial clustering of disease

Q-Q plot for uniformly distributed random variable

Power for population-based association design