R/sp.gwas-package.R

In statpng/sp.gwas: An integrated tool for an analysis of high-dimensional genomic data in Genome-Wide Association Study

#' sp.gwas
#'
#' @name sp.gwas-package
#' @docType package
#' @title Selection probabilities using generalized linear model with regularization for a SNP data in the hapmap format.
#' @details The penalty function of \code{elastic-net} is defined as \deqn{\alpha||\beta||_1+(1-\alpha)||\beta||_2/2,} where \eqn{\alpha} is a mixing proportion of ridge and the lasso, and \eqn{\beta} is regression coefficients. This penalty is equivalent to the Lasso penalty if \code{alpha=1}. \cr
#' @return A list of data files(genotype, phenotype, etc.), results for selection probabilities, and manhattan plot for multiple traits.

#' @references Zou, H., & Hastie, T. (2005). Regularization and variable selection via the elastic net. Journal of the royal statistical society: series B (statistical methodology), 67(2), 301-320.

#' @keywords hapmap gwas regularization "selection probabilities"


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