gap: Genetic analysis package
In gap: Genetic Analysis Package

gap	R Documentation

Genetic analysis package

Description

As is first reported, it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Details

We have incorporated functions for a wide range of problems as shown below.


ANALYSIS

AE3	AE model using nuclear family trios
bt	Bradley-Terry model for contingency table
ccsize	Power and sample size for case-cohort design
cs	Credibel set
fbsize	Sample size for family-based linkage and association design
gc.em	Gene counting for haplotype analysis
gcontrol	genomic control
gcontrol2	genomic control based on p values
gcp	Permutation tests using GENECOUNTING
gc.lambda	Estimation of the genomic control inflation statistic (lambda)
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
htr	Haplotype trend regression
h2.jags	Heritability estimation based on genomic relationship matrix using JAGS
hwe	Hardy-Weinberg equilibrium test for a multiallelic marker
hwe.cc	A likelihood ratio test of population Hardy-Weinberg equilibrium
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
LD22	LD statistics for two diallelic markers
LDkl	LD statistics for two multiallelic markers
lambda1000	A standardized estimate of the genomic inflation scaling to
	a study of 1,000 cases and 1,000 controls
log10p	log10(p) for a standard normal deviate
log10pvalue	log10(p) for a P value including its scientific format
logp	log(p) for a normal deviate
masize	Sample size calculation for mediation analysis
MCMCgrm	Mixed modeling with genetic relationship matrices
mia	multiple imputation analysis for hap
mr	Mendelian randomization analysis
mtdt	Transmission/disequilibrium test of a multiallelic marker
mtdt2	Transmission/disequilibrium test of a multiallelic marker
	by Bradley-Terry model
mvmeta	Multivariate meta-analysis based on generalized least squares
pbsize	Power for population-based association design
pbsize2	Power for case-control association design
pfc	Probability of familial clustering of disease
pfc.sim	Probability of familial clustering of disease
pgc	Preparing weight for GENECOUNTING
print.hap.score	Print a hap.score object
s2k	Statistics for 2 by K table
sentinels	Sentinel identification from GWAS summary statistics
tscc	Power calculation for two-stage case-control design

GRAPHICS

asplot	Regional association plot
ESplot	Effect-size plot
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
cnvplot	genomewide plot of CNVs
labelManhattan	Annotate Manhattan or Miami Plot
makeRLEplot	make relative log expression plot
METAL_forestplot	forest plot as R/meta's forest for METAL outputs
mhtplot	Manhattan plot
mhtplot2	Manhattan plot with annotations
mhtplot.trunc	truncated Manhattan plot
miamiplot	Miami plot
miamiplot2	Miami plot
mr_forestplot	Mendelian Randomization forest plot
pedtodot	Converting pedigree(s) to dot file(s)
pedtodot_verbatim	Pedigree-drawing with graphviz
plot.hap.score	Plot haplotype frequencies versus haplotype score statistics
qqfun	Quantile-comparison plots
qqunif	Q-Q plot for uniformly distributed random variable
qtl2dplot	2D QTL plot
qtl2dplotly	2D QTL plotly
qtl3dplotly	3D QTL plotly

UTITLITIES

SNP	Functions for single nucleotide polymorphisms (SNPs)
BFDP	Bayesian false-discovery probability
FPRP	False-positive report probability
ab	Test/Power calculation for mediating effect
b2r	Obtain correlation coefficients and their variance-covariances
chow.test	Chow's test for heterogeneity in two regressions
chr_pos_a1_a2	Form SNPID from chromosome, posistion and alleles
ci2ms	Effect size and standard error from confidence interval
cis.vs.trans.classification	a cis/trans classifier
comp.score	score statistics for testing genetic linkage of quantitative trait
GRM functions	ReadGRM, ReadGRMBin, ReadGRMPLINK, ReadGRMPCA, WriteGRM,
	WriteGRMBin, WriteGRMSAS
	handle genomic relationship matrix involving other software
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
h2G	A utility function for heritability
h2GE	A utility function for heritability involving gene-environment interaction
h2l	A utility function for converting observed heritability to its counterpart
	under liability threshold model
h2_mzdz	Heritability estimation according to twin correlations
klem	Haplotype frequency estimation based on a genotype table
	of two multiallelic markers
makeped	A function to prepare pedigrees in post-MAKEPED format
metap	Meta-analysis of p values
metareg	Fixed and random effects model for meta-analysis
muvar	Means and variances under 1- and 2- locus (diallelic) QTL model
qtlClassifier	A QTL cis/trans classifier
read.ms.output	A utility function to read ms output
revStrand	Allele on the reverse strand
runshinygap	Start shinygap
snptest_sample	A utility to generate SNPTEST sample file
whscore	Whittemore-Halpern scores for allele-sharing
weighted.median	Weighted median with interpolation

Usage

Vignettes on package usage:

Genetic Analysis Package. vignette("gap").
Shiny for Genetic Analysis Package (gap) Designs. vignette("shinygap").
JSS paper: Genetic Analysis Package. vignette("jss").

Author(s)

Jing Hua Zhao in collaboration with other colleagues and with help from Kurt Hornik, Brian Ripley, Uwe Ligges and Achim Zeileis

maitained by Jing Hua Zhao jinghuazhao@hotmail.com

References

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zhao07gap