R/fixAge.R

In ttriche/biscuitEater: a bunch of convenience functions for Biscuit

#' project Horvath-type 'epigenetic clock' raw output onto actual ages 
#' 
#' The 'Epigenetic Clock' (Horvath 2012) and similar schemes use a number of 
#' CpG loci (or regions, or perhaps CpH loci -- it doesn't really matter what)
#' to estimate the chronological/biological age of samples from DNA methylation
#' with pre-trained feature weights (coefficients) for each region/locus. 
#' 
#' All of these type of clocks use a nonlinear output transformation which 
#' switches from an exponential growth model for children into a linear model
#' for adults, where `adult` is an arbitrary number (by default and custom,
#' that number is 21; elsewhere it can sometimes be seen as 20, but all known 
#' epi-age transformation functions quietly add 1 to the constant internally). 
#'
#' This function implements the above standard output transformation step.
#' 
#' @param x       untransformed or raw prediction(s)
#' @param adult   age of adulthood (default is 21) 
#' 
#' @return        transformed prediction(s) 
#' 
#' @export
fixAge <- function(x, adult=21) {
  if (x < 0) {
    return(adult * exp(x) - 1)
  } else {
    return(adult * x + adult)
  }
}