gap-package {gap}R Documentation

Genetic analysis package

Description

This is 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 ACE/ADE/AE/CE 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.

Details

Package: gap
Version: 1.0-13
Depends: R(>= 2.0.0)
Suggests: Design, Hmisc, haplo.stats
License: Programs included in this package by Jing Hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors.
URL: http://www.mrc-epid.cam.ac.uk/~jinghua.zhao

Index:

BFDP                    Bayesian false-discovery probability
FPRP                    False-positive report probability
aldh2                   ALDH2 markers and Alcoholism
apoeapoc                APOE/APOC1 markers and Schizophrenia
bt                      Bradley-Terry model for contingency table
ccsize                  Power and sample size for case-cohort design
chow.test               Chow's test for heterogeneity in two regressions
cf                      Cystic Fibrosis data
comp.score              score statistics for testing genetic linkage of quantitative trait
crohn                   Crohn disease data
fa                      Friedreich Ataxia data
fbsize                  Sample size for family-based linkage and association design
fsnps                   A case-control data involving four SNPs with missing genotype
gc.em                   Gene counting for haplotype analysis
gcontrol                genomic control
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
hla                     HLA markers and Schizophrenia
htr                     Haplotype trend regression
hwe                     Hardy-Weinberg equlibrium test for multiallelic marker
hwe.hardy               Hardy-Weinberg equlibrium test using MCMC
kbyl                    LD statistics for two multiallelic loci
kin.morgan              kinship matrix for simple pedigree
makeped                 A function to prepare pedigrees in post-MAKEPED format
mao                     A study of Parkinson's disease and MAO gene
mia                     multiple imputation analysis for hap
mtdt                    Transmission/disequilibrium test of a multiallelic marker
muvar                   Means and variances under 1- and 2- locus (biallelic) QTL model
nep499                  A study of Alzheimer's disease with eight SNPs and APOE
pbsize                  Power for population-based association design
pedtodot                Converting pedigree(s) to dot file(s)
pfc                     Probability of familial clustering of disease
pfc.sim                 Probability of familial clustering of disease
pgc                     Preparing weight for GENECOUNTING
plot.hap.score          Plot Haplotype Frequencies versus Haplotype Score Statistics
print.hap.score         Print a hap.score object
qqunif                  Q-Q plot for uniformly distributed random variable
s2k                     Statistics for 2 by K table
snca                    A study of Parkinson's disease and SNCA makers
tbyt                    LD statistics for two SNPs
tscc                    Power calculation for two-stage case-control design
twinan90                Classic twin models
whscore                 Whittemore-Halpern scores for allele-sharing

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.

Author(s)

Author: Jing Hua Zhao in collaboration with other colleagues, and with help from Kurt Hornik and Brian Ripley of the R core development team

Maintainer: Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

References

Zhao JH, gap: genetic analysis package. Journal of Statistical Software.


[Package gap version 1.0-13 Index]