Genetic analysis package


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Documentation for package ‘gap’ version 1.0-17

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gap-package Genetic analysis package
aldh2 ALDH2 markers and Alcoholism
apoeapoc APOE/APOC1 markers and schizophrenia
asplot Regional association plot
BFDP Bayesian false-discovery probability
bt Bradley-Terry model for contingency table
ccsize Power and sample size for case-cohort design
CDKN Example data for association plot
CDKNgenes Example data for association plot
CDKNlocus Example data for association plot
CDKNmap Example data for association plot
cf Cystic fibrosis data
chow.test Chow's test for heterogeneity in two regressions
comp.score score statistics for testing genetic linkage of quantitative trait
crohn Crohn's disease data
ESplot Effect-size plot
fa Friedreich Ataxia data
fbsize Sample size for family-based linkage and association design
FPRP False-positive report probability
fsnps A case-control data involving four SNPs with missing genotype
gap Genetic analysis package
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
hla The HLA data
htr Haplotype trend regression
hwe Hardy-Weinberg equlibrium test for a multiallelic marker
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
makeped A function to prepare pedigrees in post-MAKEPED format
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
mhtplot Manhattan plot of p values
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
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
pm Permutation tests using GENECOUNTING
pmplus Permutation tests using GENECOUNTING
print.hap.score Print a hap.score object
qqfun Quantile-comparison plots
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
SNP Functions for single nucleotide polymorphisms (SNPs)
snp.ES Functions for single nucleotide polymorphisms (SNPs)
snp.HWE Functions for single nucleotide polymorphisms (SNPs)
snp.PAR Functions for single nucleotide polymorphisms (SNPs)
tscc Power calculation for two-stage case-control design
twinan90 Classic twin models
whscore Whittemore-Halpern scores for allele-sharing