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gap (version 1.2.3-1)

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. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

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Install

install.packages('gap')

Monthly Downloads

13,389

Version

1.2.3-1

License

GPL (>= 2)

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Repository

https://github.com/jinghuazhao/R

Maintainer

Last Published

April 21st, 2021

Functions in gap (1.2.3-1)

Mixed modeling with genetic relationship matrices

Effect-size plot

Bayesian false-discovery probability

Score statistics for association of traits with haplotypes

Functions for single nucleotide polymorphisms (SNPs)

Bradley-Terry model for contingency table

Gene counting for haplotype analysis

Power and sample size for case-cohort design

METAL_forestplot

forest plot as R/meta's forest for METAL outputs

Multivariate meta-analysis based on generalized least squares

A function to prepare pedigrees in post-MAKEPED format

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

Power for population-based association design

False-positive report probability

Truncated Manhattan plot

score statistics for testing genetic linkage of quantitative trait

Heritability estimation according to twin correlations

Kinship coefficient and genetic index of familiality

Chow's test for heterogeneity in two regressions

Regional association plot

Manhattan plot with annotations

Obtain correlation coefficients and their variance-covariances

Haplotype trend regression

Test/Power calculation for mediating effect

Sample size for family-based linkage and association design

Genetic analysis package

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

LD statistics for two multiallelic markers

Gene counting for haplotype analysis

Hardy-Weinberg equilibrium test using MCMC

genomic control based on p values

Permutation tests using GENECOUNTING

genomic control

Hardy-Weinberg equlibrium test for a multiallelic marker

Gene counting for haplotype analysis

Q-Q plot for uniformly distributed random variable

Transmission/disequilibrium test of a multiallelic marker

Sentinel identification from GWAS summary statistics

multiple imputation analysis for hap

Statistics for 2 by K table

A utility function to read ms output

Preparing weight for GENECOUNTING

Probability of familial clustering of disease

Sample size calculation for mediation analysis

Power for case-control association design

Heritability estimation based on genomic relationship matrix using JAGS

Meta-analysis of p values

Internal functions for gap

Haplotype reconstruction

Fixed and random effects model for meta-analysis

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

Converting pedigree(s) to dot file(s)

kinship matrix for simple pedigree

Probability of familial clustering of disease

Plot haplotype frequencies versus haplotype score statistics

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

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

Quantile-comparison plots

print.hap.score

Print a hap.score object

Power calculation for two-stage case-control design

Whittemore-Halpern scores for allele-sharing

LD statistics for two diallelic markers

AE model using nuclear family trios