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Install
install.packages('gap')
Monthly Downloads
5,148
Version
1.1-17
License
GPL (>= 2)
Maintainer
Jing Zhao
Last Published
April 19th, 2017
Functions in gap (1.1-17)
Search functions
CDKN
Example data for association plot
ESplot
Effect-size plot
AE3
AE model using nuclear family trios
BFDP
Bayesian false-discovery probability
PD
A study of Parkinson's disease and APOE, LRRK2, SNCA makers
SNP
Functions for single nucleotide polymorphisms (SNPs)
FPRP
False-positive report probability
LD22
LD statistics for two diallelic markers
LDkl
LD statistics for two multiallelic markers
MCMCgrm
Mixed modeling with genetic relationship matrices
b2r
Obtain correlation coefficients and their variance-covariances
bt
Bradley-Terry model for contingency table
ccsize
Power and sample size for case-cohort design
cf
Cystic fibrosis data
gc.em
Gene counting for haplotype analysis
gcontrol
genomic control
hla
The HLA data
apoeapoc
APOE/APOC1 markers and Alzheimer's
asplot
Regional association plot
fbsize
Sample size for family-based linkage and association design
gap-internal
Internal functions for gap
gap-package
Genetic analysis package
htr
Haplotype trend regression
hr1420
An example data for Manhattan plot with annotation
kin.morgan
kinship matrix for simple pedigree
klem
Haplotype frequency estimation based on a genotype table of two multiallelic markers
chow.test
Chow's test for heterogeneity in two regressions
comp.score
score statistics for testing genetic linkage of quantitative trait
gcp
Permutation tests using GENECOUNTING
mfblong
Example data for ACEnucfam
mhtdata
An example data for Manhattan plot
pbsize
Power for population-based association design
gcontrol2
genomic control based on p values
ab
Test/Power calculation for mediating effect
aldh2
ALDH2 markers and Alcoholism
crohn
Crohn's disease data
h2
Heritability estimation according to twin correlations
hap
Haplotype reconstruction
l51
An example pedigree data
lukas
An example pedigree
hwe
Hardy-Weinberg equlibrium test for a multiallelic marker
genecounting
Gene counting for haplotype analysis
gif
Kinship coefficient and genetic index of familiality
hwe.cc
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
hwe.hardy
Hardy-Weinberg equilibrium test using MCMC
pfc.sim
Probability of familial clustering of disease
pgc
Preparing weight for GENECOUNTING
mhtplot
Manhattan plot
mhtplot2
Manhattan plot with annotations
fa
Friedreich Ataxia data
hap.em
Gene counting for haplotype analysis
hap.score
Score statistics for association of traits with haplotypes
masize
Sample size calculation for mediation analysis
mia
multiple imputation analysis for hap
mtdt
Transmission/disequilibrium test of a multiallelic marker
metap
Meta-analysis of p values
metareg
Fixed and random effects model for meta-analysis
meyer
A pedigree data on 282 animals deriving from two generations
plot.hap.score
Plot haplotype frequencies versus haplotype score statistics
print.hap.score
Print a hap.score object
mvmeta
Multivariate meta-analysis based on generalized least squares
nep499
A study of Alzheimer's disease with eight SNPs and APOE
read.ms.output
A utility function to read ms output
pbsize2
Power for case-control association design
fsnps
A case-control data involving four SNPs with missing genotype
makeped
A function to prepare pedigrees in post-MAKEPED format
mao
A study of Parkinson's disease and MAO gene
mtdt2
Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model
pedtodot
Converting pedigree(s) to dot file(s)
pfc
Probability of familial clustering of disease
tscc
Power calculation for two-stage case-control design
whscore
Whittemore-Halpern scores for allele-sharing
s2k
Statistics for 2 by K table
muvar
Means and variances under 1- and 2- locus (biallelic) QTL model
qqfun
Quantile-comparison plots
qqunif
Q-Q plot for uniformly distributed random variable