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#' Genetic analysis package
#'
#' 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.
#'
#' \tabular{ll}{
#' \cr
#' \strong{ANALYSIS}\cr
#' \cr
#' AE3 \tab AE model using nuclear family trios\cr
#' bt \tab Bradley-Terry model for contingency table\cr
#' ccsize \tab Power and sample size for case-cohort design\cr
#' cs \tab Credibel set\cr
#' fbsize \tab Sample size for family-based linkage and association design\cr
#' gc.em \tab Gene counting for haplotype analysis\cr
#' gcontrol \tab genomic control\cr
#' gcontrol2 \tab genomic control based on p values\cr
#' gcp \tab Permutation tests using GENECOUNTING\cr
#' gc.lambda \tab Estimation of the genomic control inflation statistic (lambda)\cr
#' genecounting \tab Gene counting for haplotype analysis\cr
#' gif \tab Kinship coefficient and genetic index of familiality\cr
#' hap \tab Haplotype reconstruction\cr
#' hap.em \tab Gene counting for haplotype analysis\cr
#' hap.score \tab Score statistics for association of traits with haplotypes\cr
#' htr \tab Haplotype trend regression\cr
#' h2.jags \tab Heritability estimation based on genomic relationship matrix using JAGS\cr
#' hwe \tab Hardy-Weinberg equilibrium test for a multiallelic marker\cr
#' hwe.cc \tab A likelihood ratio test of population Hardy-Weinberg equilibrium \cr
#' hwe.hardy \tab Hardy-Weinberg equilibrium test using MCMC\cr
#' hwe.jags \tab Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS\cr
#' invnormal \tab inverse Normal transformation\cr
#' kin.morgan \tab kinship matrix for simple pedigree\cr
#' LD22 \tab LD statistics for two diallelic markers\cr
#' LDkl \tab LD statistics for two multiallelic markers\cr
#' lambda1000 \tab A standardized estimate of the genomic inflation scaling to\cr
#' \tab a study of 1,000 cases and 1,000 controls\cr
#' log10p \tab log10(p) for a standard normal deviate\cr
#' log10pvalue \tab log10(p) for a P value including its scientific format\cr
#' logp \tab log(p) for a normal deviate\cr
#' masize \tab Sample size calculation for mediation analysis\cr
#' MCMCgrm \tab Mixed modeling with genetic relationship matrices\cr
#' mia \tab multiple imputation analysis for hap\cr
#' mr \tab Mendelian randomization analysis\cr
#' mtdt \tab Transmission/disequilibrium test of a multiallelic marker\cr
#' mtdt2 \tab Transmission/disequilibrium test of a multiallelic marker\cr
#' \tab by Bradley-Terry model\cr
#' mvmeta \tab Multivariate meta-analysis based on generalized least squares\cr
#' pbsize \tab Power for population-based association design\cr
#' pbsize2 \tab Power for case-control association design\cr
#' pfc \tab Probability of familial clustering of disease\cr
#' pfc.sim \tab Probability of familial clustering of disease\cr
#' pgc \tab Preparing weight for GENECOUNTING\cr
#' print.hap.score \tab Print a hap.score object\cr
#' s2k \tab Statistics for 2 by K table\cr
#' sentinels \tab Sentinel identification from GWAS summary statistics\cr
#' tscc \tab Power calculation for two-stage case-control design\cr
#' \cr
#' \strong{GRAPHICS}\cr
#' \cr
#' asplot \tab Regional association plot\cr
#' ESplot \tab Effect-size plot\cr
#' circos.cis.vs.trans.plot \tab circos plot of cis/trans classification\cr
#' circos.cnvplot \tab circos plot of CNVs\cr
#' circos.mhtplot \tab circos Manhattan plot with gene annotation\cr
#' circos.mhtplot2 \tab Another circos Manhattan plot\cr
#' cnvplot \tab genomewide plot of CNVs\cr
#' labelManhattan \tab Annotate Manhattan or Miami Plot\cr
#' makeRLEplot \tab make relative log expression plot\cr
#' METAL_forestplot \tab forest plot as R/meta's forest for METAL outputs\cr
#' mhtplot \tab Manhattan plot\cr
#' mhtplot2 \tab Manhattan plot with annotations\cr
#' mhtplot.trunc \tab truncated Manhattan plot\cr
#' miamiplot \tab Miami plot\cr
#' miamiplot2 \tab Miami plot\cr
#' mr_forestplot \tab Mendelian Randomization forest plot\cr
#' pedtodot \tab Converting pedigree(s) to dot file(s)\cr
#' pedtodot_verbatim \tab Pedigree-drawing with graphviz\cr
#' plot.hap.score \tab Plot haplotype frequencies versus haplotype score statistics\cr
#' qqfun \tab Quantile-comparison plots\cr
#' qqunif \tab Q-Q plot for uniformly distributed random variable\cr
#' qtl2dplot \tab 2D QTL plot\cr
#' qtl2dplotly \tab 2D QTL plotly\cr
#' qtl3dplotly \tab 3D QTL plotly\cr
#' \cr
#' \strong{UTITLITIES}\cr
#' \cr
#' SNP \tab Functions for single nucleotide polymorphisms (SNPs)\cr
#' BFDP \tab Bayesian false-discovery probability\cr
#' FPRP \tab False-positive report probability\cr
#' ab \tab Test/Power calculation for mediating effect\cr
#' b2r \tab Obtain correlation coefficients and their variance-covariances\cr
#' chow.test \tab Chow's test for heterogeneity in two regressions\cr
#' chr_pos_a1_a2 \tab Form SNPID from chromosome, posistion and alleles\cr
#' ci2ms \tab Effect size and standard error from confidence interval\cr
#' cis.vs.trans.classification \tab a cis/trans classifier\cr
#' comp.score \tab score statistics for testing genetic linkage of quantitative trait\cr
#' GRM functions \tab ReadGRM, ReadGRMBin, ReadGRMPLINK, ReadGRMPCA, WriteGRM,\cr
#' \tab WriteGRMBin, WriteGRMSAS\cr
#' \tab handle genomic relationship matrix involving other software\cr
#' get_b_se \tab Get b and se from AF, n, and z\cr
#' get_pve_se \tab Get pve and its standard error from n, z\cr
#' get_sdy \tab Get sd(y) from AF, n, b, se\cr
#' h2G \tab A utility function for heritability\cr
#' h2GE \tab A utility function for heritability involving gene-environment interaction\cr
#' h2l \tab A utility function for converting observed heritability to its counterpart\cr
#' \tab under liability threshold model\cr
#' h2_mzdz \tab Heritability estimation according to twin correlations\cr
#' klem \tab Haplotype frequency estimation based on a genotype table\cr
#' \tab of two multiallelic markers\cr
#' makeped \tab A function to prepare pedigrees in post-MAKEPED format\cr
#' metap \tab Meta-analysis of p values\cr
#' metareg \tab Fixed and random effects model for meta-analysis\cr
#' muvar \tab Means and variances under 1- and 2- locus (diallelic) QTL model\cr
#' qtlClassifier \tab A QTL cis/trans classifier\cr
#' qtlFinder \tab Distance-based signal identification\cr
#' read.ms.output \tab A utility function to read ms output\cr
#' revStrand \tab Allele on the reverse strand\cr
#' runshinygap \tab Start shinygap\cr
#' snptest_sample \tab A utility to generate SNPTEST sample file\cr
#' whscore \tab Whittemore-Halpern scores for allele-sharing\cr
#' weighted.median \tab Weighted median with interpolation\cr
#' \cr
#' }
#'
#' @section 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")`.
#'
#' @docType package
#' @name gap
#' @aliases gap-package
#'
#' @import dplyr gap.datasets
#' @importFrom grDevices dev.off palette pdf xy.coords
#' @importFrom graphics abline arrows axis box boxplot
#' identify legend lines mtext par points
#' segments text title
#' @importFrom stats as.formula coef coefficients cor
#' complete.cases dnorm glm integrate lm median
#' nlm pchisq pf pnorm ppoints pt qchisq qnorm
#' qqplot qt quantile rbinom rexp rnorm
#' runif sd setNames var
#' @importFrom utils data head packageDescription read.csv
#' read.delim read.table tail write.table
#' globalVariables
#' @importFrom Rdpack reprompt
#' @useDynLib gap
#'
#' @author 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
#' \insertRef{zhao07}{gap}
#'
#' @keywords internal
"_PACKAGE"
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