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gap (version 1.0-14)

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

1.0-14

License

GPL (>=2)

Maintainer

Jing Zhao

Last Published

August 27th, 2024

Functions in gap (1.0-14)

bt

Bradley-Terry model for contingency table
htr

Haplotype trend regression
aldh2

ALDH2 markers and Alcoholism
kin.morgan

kinship matrix for simple pedigree
gcontrol

genomic control
gcp

Permutation tests using GENECOUNTING
genecounting

Gene counting for haplotype analysis
hwe

Hardy-Weinberg equlibrium test for a multiallelic marker
crohn

Crohn's disease data
apoeapoc

APOE/APOC1 markers and schizophrenia
gif

Kinship coefficient and genetic index of familiality
cf

Cystic fibrosis data
gc.em

Gene counting for haplotype analysis
comp.score

score statistics for testing genetic linkage of quantitative trait
chow.test

Chow's test for heterogeneity in two regressions
gap-package

Genetic analysis package
gap-internal

internal functions for gap
BFDP

Bayesian false-discovery probability
hap

Haplotype reconstruction
fbsize

Sample size for family-based linkage and association design
hla

The HLA data
FPRP

False-positive report probability
ccsize

Power and sample size for case-cohort design
fsnps

A case-control data involving four SNPs with missing genotype
hap.score

Score statistics for association of traits with haplotypes
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
s2k

Statistics for 2 by K table
mtdt

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

Print a hap.score object
tbyt

LD statistics for two SNPs
twinan90

Classic twin models
qqunif

Q-Q plot for uniformly distributed random variable
pfc

Probability of familial clustering of disease
pbsize2

Power for case-control association design
mia

multiple imputation analysis for hap
plot.hap.score

Plot haplotype frequencies versus haplotype score statistics
muvar

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

A study of Parkinson's disease and SNCA makers
pgc

Preparing weight for GENECOUNTING
pbsize

Power for population-based association design
makeped

A function to prepare pedigrees in post-MAKEPED format
pfc.sim

Probability of familial clustering of disease
tscc

Power calculation for two-stage case-control design
fa

Friedreich Ataxia data
nep499

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

A study of Parkinson's disease and MAO gene
whscore

Whittemore-Halpern scores for allele-sharing
kbyl

LD statistics for two multiallelic loci
hap.em

Gene counting for haplotype analysis
pedtodot

Converting pedigree(s) to dot file(s)