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

gap (version 1.0-22)

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.

Copy Link

Version

Install

install.packages('gap')

Monthly Downloads

15,115

Version

1.0-22

License

GPL (>= 2)

Maintainer

Jing Zhao

Last Published

January 2nd, 2010

Functions in gap (1.0-22)

hap.score

Score statistics for association of traits with haplotypes
SNP

Functions for single nucleotide polymorphisms (SNPs)
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
aldh2

ALDH2 markers and Alcoholism
asplot

Regional association plot
htr

Haplotype trend regression
mhtplot

Manhattan plot of p values
plot.hap.score

Plot haplotype frequencies versus haplotype score statistics
hla

The HLA data
fsnps

A case-control data involving four SNPs with missing genotype
fa

Friedreich Ataxia data
twinan90

Classic twin models
cf

Cystic fibrosis data
qqfun

Quantile-comparison plots
FPRP

False-positive report probability
apoeapoc

APOE/APOC1 markers and schizophrenia
hap.em

Gene counting for haplotype analysis
ESplot

Effect-size plot
pfc

Probability of familial clustering of disease
metareg

Fixed and random effects model for meta-analysis
makeped

A function to prepare pedigrees in post-MAKEPED format
LD22

LD statistics for two diallelic markers
hap

Haplotype reconstruction
gcp

Permutation tests using GENECOUNTING
ccsize

Power and sample size for case-cohort design
metap

Meta-analysis of p values
pfc.sim

Probability of familial clustering of disease
pbsize2

Power for case-control association design
gcontrol

genomic control
comp.score

score statistics for testing genetic linkage of quantitative trait
read.ms.output

A utility function to read ms output
LDkl

LD statistics for two multiallelic markers
mia

multiple imputation analysis for hap
nep499

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

Q-Q plot for uniformly distributed random variable
abc

Test/Power calculation for mediating effect
gcontrol2

genomic control based on p values
mvmeta

Multivariate meta-analysis based on generalized least squares
s2k

Statistics for 2 by K table
bt

Bradley-Terry model for contingency table
BFDP

Bayesian false-discovery probability
crohn

Crohn's disease data
gap-package

Genetic analysis package
gap-internal

Internal functions for gap
gc.em

Gene counting for haplotype analysis
mao

A study of Parkinson's disease and MAO gene
hwe

Hardy-Weinberg equlibrium test for a multiallelic marker
muvar

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

kinship matrix for simple pedigree
whscore

Whittemore-Halpern scores for allele-sharing
pgc

Preparing weight for GENECOUNTING
pbsize

Power for population-based association design
print.hap.score

Print a hap.score object
tscc

Power calculation for two-stage case-control design
snca

A study of Parkinson's disease and SNCA makers
CDKN

Example data for association plot
pedtodot

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

Transmission/disequilibrium test of a multiallelic marker
b2r

Obtain correlation coefficients and their variance-covariances
fbsize

Sample size for family-based linkage and association design
chow.test

Chow's test for heterogeneity in two regressions
genecounting

Gene counting for haplotype analysis
gif

Kinship coefficient and genetic index of familiality