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gap (version 1.0-20)

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, classic twin models, 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

1.0-20

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

August 26th, 2009

Functions in gap (1.0-20)

ESplot

Effect-size plot
cf

Cystic fibrosis data
LDkl

LD statistics for two multiallelic markers
chow.test

Chow's test for heterogeneity in two regressions
mvmeta

Multivariate meta-analysis based on generalized least squares
b2r

Obtain correlation coefficients and their variance-covariances
qqfun

Quantile-comparison plots
BFDP

Bayesian false-discovery probability
comp.score

score statistics for testing genetic linkage of quantitative trait
hwe

Hardy-Weinberg equlibrium test for a multiallelic marker
metareg

Fixed and random effects model for meta-analysis
aldh2

ALDH2 markers and Alcoholism
gcp

Permutation tests using GENECOUNTING
hap

Haplotype reconstruction
fa

Friedreich Ataxia data
CDKN

Example data for association plot
bt

Bradley-Terry model for contingency table
plot.hap.score

Plot haplotype frequencies versus haplotype score statistics
metap

Meta-analysis of p values
apoeapoc

APOE/APOC1 markers and schizophrenia
fbsize

Sample size for family-based linkage and association design
htr

Haplotype trend regression
LD22

LD statistics for two diallelic markers
gcontrol2

genomic control based on p values
gc.em

Gene counting for haplotype analysis
asplot

Regional association plot
crohn

Crohn's disease data
twinan90

Classic twin models
qqunif

Q-Q plot for uniformly distributed random variable
gcontrol

genomic control
FPRP

False-positive report probability
mia

multiple imputation analysis for hap
gap-package

Genetic analysis package
pfc

Probability of familial clustering of disease
nep499

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

Hardy-Weinberg equilibrium test using MCMC
tscc

Power calculation for two-stage case-control design
pfc.sim

Probability of familial clustering of disease
gif

Kinship coefficient and genetic index of familiality
pbsize2

Power for case-control association design
print.hap.score

Print a hap.score object
muvar

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

Preparing weight for GENECOUNTING
SNP

Functions for single nucleotide polymorphisms (SNPs)
hap.score

Score statistics for association of traits with haplotypes
hla

The HLA data
whscore

Whittemore-Halpern scores for allele-sharing
makeped

A function to prepare pedigrees in post-MAKEPED format
fsnps

A case-control data involving four SNPs with missing genotype
gap-internal

Internal functions for gap
genecounting

Gene counting for haplotype analysis
kin.morgan

kinship matrix for simple pedigree
mtdt

Transmission/disequilibrium test of a multiallelic marker
pbsize

Power for population-based association design
pedtodot

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

A study of Parkinson's disease and MAO gene
ccsize

Power and sample size for case-cohort design
hap.em

Gene counting for haplotype analysis
mhtplot

Manhattan plot of p values
s2k

Statistics for 2 by K table
snca

A study of Parkinson's disease and SNCA makers