R/coefSNPreg.R

In FunctanSNP: Functional Analysis (with Interactions) for Dense SNP Data

##' @title Extract coefficients from an SNPlm or SNPinter object
##'
##' @description This functions predicts coefficients and related coefficient functions from a fitted "SNPlm" or "SNPinter" object.
##'
##' @param x an "SNPlm"/"SNPinter" object obtained by \code{\link{SNPlm}}/\code{\link{SNPinter}}.
##'
##' @return An "coef.SNPreg" object that contains the list of the following items.
##' \itemize{
##' \item{alpha:}{ estimated intercept value.}
##' \item{gamma:}{ estimated coefficients of the scalar covariates.}
##' \item{b:}{ estimated coefficients of the chosen basis functions for the genetic effect function beta(t) (and interaction items betak(t), if x is an "SNPinter" object).}
##' \item{betat:}{ an "fd" object, representing the estimated genetic effect function beta(t).}
##' }
##'
##' @seealso See Also as \code{\link{SNPlm}}, \code{\link{SNPinter}}.
##'
##' @export
##' @examples
##' library(FunctanSNP)
##' n <- 300
##' m <- 30
##' simdata1 <- simData1(n, m, seed = 123)
##' SNPlmres <- SNPlm(y = simdata1$y, z = simdata1$z,
##'                   location = simdata1$location, X = simdata1$X,
##'                   type1 = "Bspline", type2 = "Bspline", nbasis1 = 5,
##'                   nbasis2 = 5, params1 = 4, params2 = 4,
##'                   intercept = FALSE, Plot = FALSE)
##' coef1 <- coefSNPreg(x = SNPlmres)
##' coef1$alpha ###intercept
##' coef1$gamma ###coefficients of scalar variables
##' coef1$b     ###coefficients of basis functions
##'
##' simdata2 <- simData2(n, m, seed = 123)
##' lambda1 <- 0.05
##' lambda2 <- sqrt(3)*lambda1
##' eta <- 0
##' SNPinterres <- SNPinter(y = simdata2$y, z = simdata2$z,
##'                         location = simdata2$location, X = simdata2$X,
##'                         lambda1, lambda2, eta, type1 = "Bspline", nbasis1 = 5,
##'                         params1 = 4, Bsplines = 5, norder = 4, intercept = TRUE,
##'                         eps = 1e-2, maxstep = 1e2, Plot = FALSE)
##' coef2 <- coefSNPreg(x = SNPinterres)
##' coef2$alpha ###intercept
##' coef2$gamma ###coefficients of scalar variables
##' coef2$b     ###coefficients of basis functions
##'

coefSNPreg <- function(x){
  #x <- SNPinterres
  alpha <- x$alpha
  gamma <- x$gamma
  b <- x$b
  betat <- x$betat
  result <- list(alpha = alpha, gamma = gamma, b = b, betat = betat)
  class(result) <- "coef.SNPreg"
  return(result)
}