R/p.exact-package.R

In p.exact: Exact P-values for Genome-Wide Association Analyses in Inbred Populations

#' p.exact: Exact P-values for Genome-Wide Association Analyses in Inbred Populations
#' 
#' The p.exact package implements for calculating exact dataset-specific p-values for 
#' genome-wide association (GWA) analyses in inbred populations. The module is 
#' compatible with existing GenABEL/gwaa.data data formats. 
#' 
#' For converting data from other formats, see
#' 
#' \code{\link{convert.snp.illumina}} (Illumina/Affymetrix-like format).
#' \code{\link{convert.snp.text}} (conversion from human-readable GenABEL format),
#' \code{\link{convert.snp.ped}} (Linkage, Merlin, Mach, and similar files),
#' \code{\link{convert.snp.mach}} (Mach-format),
#' \code{\link{convert.snp.tped}} (from PLINK TPED format),
#' \code{\link{convert.snp.affymetrix}} (BRML-style files).
#' 
#' For converting of GenABEL's data to other formats, see
#' \code{\link{export.merlin}} (MERLIN and MACH formats), 
#' \code{\link{export.impute}} (IMPUTE, SNPTEST and CHIAMO formats),
#' \code{\link{export.plink}} (PLINK format, also exports phenotypic data). 
#' 
#' To load the data, see \code{\link{load.gwaa.data}}.
#' 
#' For data managment and manipulations see
#' \code{\link{merge.gwaa.data}},
#' \code{\link{merge.snp.data}},
#' \code{\link{gwaa.data-class}},
#' \code{\link{snp.data-class}},
#' \code{\link{snp.names}},
#' \code{\link{snp.subset}}.
#' 
#' @author Xia Shen
#' 
#' @references 
#' If you use p.exact package in your analysis, please cite the following work:
#' 
#' Xia Shen (2015).
#' Beyond permutation test: calculating exact dataset-specific p-values for 
#' genome-wide association studies in inbred populations. \emph{Submitted}.
#' 
#' @seealso \code{GenABEL}
#'
#'
#' @name p.exact
#' @docType package
#' @title Exact p-values
#' @aliases p.exact p.exact-package
#' @keywords package
#'
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