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 |