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gap (version 1.2.1)

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.

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Install

install.packages('gap')

Monthly Downloads

16,595

Version

1.2.1

License

GPL (>= 2)

Issues

4

Pull Requests

0

Stars

12

Forks

4

Maintainer

Jing Zhao

Last Published

June 5th, 2019

Functions in gap (1.2.1)

ab

Test/Power calculation for mediating effect
METAL_forestplot

forest plot as R/meta's forest for METAL outputs
AE3

AE model using nuclear family trios
MCMCgrm

Mixed modeling with genetic relationship matrices
ESplot

Effect-size plot
LDkl

LD statistics for two multiallelic markers
LD22

LD statistics for two diallelic markers
BFDP

Bayesian false-discovery probability
SNP

Functions for single nucleotide polymorphisms (SNPs)
FPRP

False-positive report probability
chow.test

Chow's test for heterogeneity in two regressions
h2.jags

Heritability estimation based on genomic relationship matrix using JAGS
comp.score

score statistics for testing genetic linkage of quantitative trait
hap

Haplotype reconstruction
fbsize

Sample size for family-based linkage and association design
hwe

Hardy-Weinberg equlibrium test for a multiallelic marker
hap.em

Gene counting for haplotype analysis
htr

Haplotype trend regression
hap.score

Score statistics for association of traits with haplotypes
gap-internal

Internal functions for gap
hwe.cc

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

Regional association plot
b2r

Obtain correlation coefficients and their variance-covariances
gif

Kinship coefficient and genetic index of familiality
bt

Bradley-Terry model for contingency table
muvar

Means and variances under 1- and 2- locus (biallelic) QTL model
mtdt2

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

Hardy-Weinberg equilibrium test using MCMC
pfc

Probability of familial clustering of disease
pfc.sim

Probability of familial clustering of disease
h2

Heritability estimation according to twin correlations
metap

Meta-analysis of p values
mhtplot.trunc

Truncated Manhattan plot
masize

Sample size calculation for mediation analysis
ccsize

Power and sample size for case-cohort design
gcontrol

genomic control
mtdt

Transmission/disequilibrium test of a multiallelic marker
plot.hap.score

Plot haplotype frequencies versus haplotype score statistics
mia

multiple imputation analysis for hap
pgc

Preparing weight for GENECOUNTING
gcontrol2

genomic control based on p values
pbsize2

Power for case-control association design
pedtodot

Converting pedigree(s) to dot file(s)
mhtplot2

Manhattan plot with annotations
kin.morgan

kinship matrix for simple pedigree
hwe.jags

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
gap-package

Genetic analysis package
metareg

Fixed and random effects model for meta-analysis
mhtplot

Manhattan plot
gc.em

Gene counting for haplotype analysis
gcp

Permutation tests using GENECOUNTING
genecounting

Gene counting for haplotype analysis
klem

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

A function to prepare pedigrees in post-MAKEPED format
print.hap.score

Print a hap.score object
mvmeta

Multivariate meta-analysis based on generalized least squares
qqfun

Quantile-comparison plots
tscc

Power calculation for two-stage case-control design
whscore

Whittemore-Halpern scores for allele-sharing
pbsize

Power for population-based association design
qqunif

Q-Q plot for uniformly distributed random variable
read.ms.output

A utility function to read ms output
s2k

Statistics for 2 by K table
sentinels

Sentinel identification from GWAS summary statistics