ll{
Package: gap
Version: 1.1-2
Depends: R(>= 2.0.0)
Suggests: BradleyTerry2, Design, Hmisc, MASS, grid, haplo.stats, magic, pedigree, survival
License: GPL (>=2)
URL: http://www.mrc-epid.cam.ac.uk/~jinghua.zhao
}Index:
ll{
BFDP Bayesian false-discovery probability
FPRP False-positive report probability
SNP Functions for single nucleotide polymorphisms (SNPs)
ab Test/Power calculation for mediating effect
aldh2 ALDH2 markers and Alcoholism
apoeapoc APOE/APOC1 markers and Alzheimer's
asplot Regional association plot
bt Bradley-Terry model for contingency table
b2r Obtain correlation coefficients and their variance-covariances
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
ESplot Effect-size plot
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
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
h2 Heritability estimation according to twin correlations
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.cc A likelihood ratio test of population Hardy-Weinberg equilibrium
for case-control studies
hwe.hardy Hardy-Weinberg equlibrium test using MCMC
kin.morgan kinship matrix for simple pedigree
klem Haplotype frequency estimation based on a genotype table
of two multiallelic markers
LD22 LD statistics for two diallelic markers
LDkl LD statistics for two multiallelic markers
makeped A function to prepare pedigrees in post-MAKEPED format
masize Sample size calculation for mediation analysis
mao A study of Parkinson's disease and MAO gene
metap Meta-analysis of p values
metareg Fixed and random effects model for meta-analysis
mhtdata An example data for Manhattan plot
mhtplot Manhattan plot of p values
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
muvar Means and variances under 1- and 2- locus (diallelic) QTL model
mvmeta Multivariate meta-analysis based on generalized least squares
nep499 A study of Alzheimer's disease with eight SNPs and APOE
pbsize Power for population-based association design
pbsize2 Power for case-control 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
qqfun Quantile-comparison plots
qqunif Q-Q plot for uniformly distributed random variable
read.ms.output A utility function to read ms output
s2k Statistics for 2 by K table
snca A study of Parkinson's disease and SNCA makers
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.