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gap (version 1.1-16)

gap-package: 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.

Arguments

Details

Package:
gap
Version:
1.1-13
Depends:
R(>= 2.1.0)
Suggests:
BradleyTerry2, MASS, Matrix, MCMCglmm, NCBI2R, bdsmatrix, coxme, foreign, grid,
haplo.stats, kinship2, magic, mets, nlme, pedigree, pedigreemm, regress, rms, survival
License:
GPL (>=2)
URL:
http://www.mrc-epid.cam.ac.uk/people/jing-hua-zhao

Index:

* ANALYSIS *
AE3
AE model using nuclear family trios
bt
Bradley-Terry model for contingency table
ccsize
Power and sample size for case-cohort design
fbsize
Sample size for family-based linkage and association design
gc.em
Gene counting for haplotype analysis
gcontrol
genomic control
gcontrol2
genomic control based on p values
gcp
Permutation tests using GENECOUNTING
genecounting
Gene counting for haplotype analysis
gif
Kinship coefficient and genetic index of familiality
hap
Haplotype reconstruction
hap.em
Gene counting for haplotype analysis
hap.score
Score statistics for association of traits with haplotypes
htr
Haplotype trend regression
hwe
Hardy-Weinberg equilibrium test for a multiallelic marker
hwe.cc
A likelihood ratio test of population Hardy-Weinberg equilibrium
hwe.hardy
Hardy-Weinberg equilibrium test using MCMC
kin.morgan
kinship matrix for simple pedigree
LD22
LD statistics for two diallelic markers
LDkl
LD statistics for two multiallelic markers
masize
Sample size calculation for mediation analysis
MCMCgrm
Mixed modeling with genetic relationship matrices
mia
multiple imputation analysis for hap
mtdt
Transmission/disequilibrium test of a multiallelic marker
mtdt2
Transmission/disequilibrium test of a multiallelic marker
by Bradley-Terry model
mvmeta
Multivariate meta-analysis based on generalized least squares
pbsize
Power for population-based association design
pbsize2
Power for case-control association design
pfc
Probability of familial clustering of disease
pfc.sim
Probability of familial clustering of disease
pgc
Preparing weight for GENECOUNTING
print.hap.score
Print a hap.score object
s2k
Statistics for 2 by K table
tscc
Power calculation for two-stage case-control design

* GRAPHICS * asplot Regional association plot ESplot Effect-size plot mhtplot Manhattan plot mhtplot2 Manhattan plot with annotations pedtodot Converting pedigree(s) to dot file(s) plot.hap.score Plot haplotype frequencies versus haplotype score statistics qqfun Quantile-comparison plots qqunif Q-Q plot for uniformly distributed random variable

* DATASETS * PD A study of Parkinson's disease and APOE, LRRK2, SNCA makers aldh2 ALDH2 markers and alcoholism apoeapoc APOE/APOC1 markers and schizophrenia cf Cystic Fibrosis data crohn Crohn's disease data fa Friedreich ataxia data fsnps A case-control data involving four SNPs with missing genotype hla HLA markers and schizophrenia l51 An example pedigree data lukas An example pedigree mao A study of Parkinson's disease and MAO gene meyer A pedigree data on 282 animals deriving from two generations nep499 A study of Alzheimer's disease with eight SNPs and APOE

* UTITLITIES * SNP Functions for single nucleotide polymorphisms (SNPs) BFDP Bayesian false-discovery probability FPRP False-positive report probability ab Test/Power calculation for mediating effect b2r Obtain correlation coefficients and their variance-covariances chow.test Chow's test for heterogeneity in two regressions comp.score score statistics for testing genetic linkage of quantitative trait h2 Heritability estimation according to twin correlations for case-control studies klem Haplotype frequency estimation based on a genotype table of two multiallelic markers makeped A function to prepare pedigrees in post-MAKEPED format metap Meta-analysis of p values metareg Fixed and random effects model for meta-analysis muvar Means and variances under 1- and 2- locus (diallelic) QTL model read.ms.output A utility function to read ms output twinan90 Classic twin models whscore Whittemore-Halpern scores for allele-sharing GRM functions ReadGRM, ReadGRMBin, ReadGRMPLINK, ReadGRMPCA, WriteGRM, WriteGRMBin, WriteGRMSAS handle genomic relationship matrix involving other software heritability functions h2G, VR, h2GC, h2l give point estimates as with their variances for continuous traits and binary traits under liability threshold model and case-control sampling

We have incorporated functions for a wide range of problems. Nevertheless, this largely remains as a preliminary work to be consolidated in the near future.

References

Zhao JH, gap: genetic analysis package. Journal of Statistical Software 2007, 23(8):1-18