R: Genetic Analysis Package

# Genetic Analysis Package

## Documentation for package ‘gap’ version 1.2.3-6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

ab | Test/Power calculation for mediating effect
AE3 | AE model using nuclear family trios
asplot | Regional association plot
b2r | Obtain correlation coefficients and their variance-covariances
BFDP | Bayesian false-discovery probability
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
circos.cis.vs.trans.plot | circos plot of cis/trans classification
circos.cnvplot | circos plot of CNVs.
circos.mhtplot | circos Manhattan plot with gene annotation
cis.vs.trans.classification | A cis/trans classifier
cnvplot | genomewide plot of CNVs
comp.score | score statistics for testing genetic linkage of quantitative trait
cs | Credible set
ESplot | Effect-size plot
fbsize | Sample size for family-based linkage and association design
FPRP | False-positive report probability
gc.em | Gene counting for haplotype analysis
gc.lambda | Estionmation of the genomic control inflation statistic (lambda)
gcontrol | genomic control
gcontrol2 | genomic control based on p values
gcp | Permutation tests using GENECOUNTING
genecounting | Gene counting for haplotype analysis
get_b_se | Get b and se from AF, n, and z
get_pve_se | Get pve and its standard error from n, z
get_sdy | Get sd(y) from AF, n, b, se
gif | Kinship coefficient and genetic index of familiality
gsmr | Mendelian randomization analysis
h2.jags | Heritability estimation based on genomic relationship matrix using JAGS
h2G | Heritability and its variance
h2GE | Heritability and its variance when there is an environment component
h2l | Heritability under the liability threshold model
h2_mzdz | 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
htr | Haplotype trend regression
hwe | Hardy-Weinberg equlibrium test for a multiallelic marker
hwe.cc | A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
hwe.hardy | Hardy-Weinberg equilibrium test using MCMC
hwe.jags | Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
invnormal | Inverse normal transformation
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
log10p | log10(p) for a normal deviate z
log10pvalue | log10(p) for a P value including its scientific format
logp | log(p) for a normal deviate z
makeped | A function to prepare pedigrees in post-MAKEPED format
masize | Sample size calculation for mediation analysis
MCMCgrm | Mixed modeling with genetic relationship matrices
METAL_forestplot | forest plot as R/meta's forest for METAL outputs
metap | Meta-analysis of p values
metareg | Fixed and random effects model for meta-analysis
mhtplot | Manhattan plot
mhtplot.trunc | Truncated Manhattan plot
mhtplot2 | Manhattan plot with annotations
mia | Multiple imputation analysis for hap
miamiplot | Miami plot
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 (biallelic) QTL model
mvmeta | Multivariate meta-analysis based on generalized least squares
PARn | Functions for single nucleotide polymorphisms (SNPs)
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
pqtl2dplot | 2D pQTL plot
pqtl2dplotly | 2D pQTL plotly
pqtl3dplotly | 3D pQTL plot
print.hap.score | Print a hap.score object
pvalue | P value for a normal deviate
qqfun | Quantile-comparison plots
qqunif | Q-Q plot for uniformly distributed random variable
read.ms.output | A utility function to read ms output
revStrand | Allele on the reverse strand
runshinygap | Start shinygap
s2k | Statistics for 2 by K table
sentinels | Sentinel identification from GWAS summary statistics
snp.ES | Functions for single nucleotide polymorphisms (SNPs)
snp.HWE | Functions for single nucleotide polymorphisms (SNPs)
snp.PAR | Functions for single nucleotide polymorphisms (SNPs)
snptest_sample | A utility to generate SNPTEST sample file
tscc | Power calculation for two-stage case-control design
whscore | Whittemore-Halpern scores for allele-sharing