# Genetic Analysis Package

## Documentation for package ‘gap’ version 1.15.2

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

## Help Pages

A B C E F G H I K L M P Q R S T W X

## -- A --

a2g | Allele-to-genotype conversion
ab | Test/Power calculation for mediating effect
ACDE | Fit AE, ACE or ADE biometric mixed models to nuclear family data
AE3 | AE model using nuclear family trios
allele.recode | Allele recoding
asplot | Regional association plot

## -- B --

b2r | Obtain correlation coefficients and their variance-covariances
BFDP | Bayesian false-discovery probability
bt | Bradley-Terry model for contingency table

## -- C --

ccsize | Power and sample size for case-cohort design
chow.test | Chow's test for heterogeneity in two regressions
chr_pos_a1_a2 | SNP id by chr:pos+a1/a2
ci2ms | Effect size and standard error from confidence interval
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
circos.mhtplot2 | Another circos Manhattan plot
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 from summary statistics

## -- E --

ESplot | Effect-size / Odds-ratio forest plot

## -- F --

fbsize | Sample size for family-based linkage and association design
FPRP | False-positive report probability

## -- G --

g2a | Conversion of a genotype identifier to alleles
gc.em | Gene counting for haplotype analysis
gc.lambda | Estimation 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
geno.recode | Genotype recoding
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
grid2d | Two-dimensional grid

## -- H --

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.control | Control for haplotype reconstruction
hap.em | Gene counting for haplotype analysis
hap.score | Score statistics for association of traits with haplotypes
hg18 | Chromosomal lengths for build 36
hg19 | Chromosomal lengths for build 37
hg38 | Chromosomal lengths for build 38
hmht.control | Controls for highlighted regions in mhtplot
htr | Haplotype trend regression
hwe | Hardy-Weinberg Equilibrium Test (Multiallelic, Unified Interface)
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

## -- I --

invnormal | Inverse normal transformation
inv_chr_pos_a1_a2 | Retrieval of chr:pos+a1/a2 according to SNP id
ixy | Conversion of chrosome name from strings

## -- K --

KCC | Disease prevalences in cases and controls
kin.morgan | kinship matrix for simple pedigree
klem | Haplotype frequency estimation based on a genotype table of two multiallelic markers

## -- L --

labelManhattan | Annotate Manhattan or Miami Plot
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

## -- M --

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 with heterogeneity and random effects
metareg | Fixed and random effects meta-analysis (vectorised implementation)
mht.control | Controls for Manhattan plot
mhtplot | Manhattan plot
mhtplot.trunc | Truncated Manhattan plot
mhtplot2 | Manhattan plot with annotations
mia | Multiple imputation analysis for hap
miamiplot | Miami plot
miamiplot2 | Miami Plot
mr | Mendelian Randomization wrapper (IVW, Egger, Weighted Median, Penalised WM)
mr_forestplot | Mendelian Randomization forest 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 fixed-effects meta-analysis via generalized least squares

## -- P --

PARn | Functions for single nucleotide polymorphisms
pbsize | Power for population-based association design
pbsize2 | Power for case-control association design
pedtodot | Converting pedigree(s) to dot file(s)
pedtodot_verbatim | Pedigree-drawing with graphviz
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
pvalue | P value for a normal deviate

## -- Q --

qqfun | Quantile-comparison plots
qqunif | Q-Q plot for uniformly distributed random variables
qtl2dplot | 2D QTL plot
qtl2dplotly | 2D QTL plotly
qtl3dplotly | 3D QTL plot
qtlClassifier | A QTL cis/trans classifier
qtlFinder | Distance-based signal identification

## -- R --

read.ms.output | A utility function to read ms output
ReadGRM | A function to read GRM file
ReadGRMBin | A function to read GRM binary files
revStrand | Allele on the reverse strand
runshinygap | Start shinygap

## -- S --

s2k | Statistics for 2 by K table
sentinels | Sentinel identification from GWAS summary statistics
snpHWE | Functions for single nucleotide polymorphisms
snpPAR | Functions for single nucleotide polymorphisms
snpPVE | Functions for single nucleotide polymorphisms
snptest_sample | A utility to generate SNPTEST sample file

## -- T --

tscc | Power calculation for two-stage case-control design

## -- W --

whscore | Whittemore-Halpern scores for allele-sharing
WriteGRM | A function to write GRM file
WriteGRMBin | A function to write GRM binary file

## -- X --

xy | Conversion of chromosome names to strings