R/horvath-age.R

In jcalendo/coriell: Convenience Functions for Bioinformatics

#' Transform ages using Horvath's method
#' 
#' Transform age in years using the log transformation defined in Horvath (2013). 
#' This function can also be used to convert transformed ages back to the 
#' original scale.
#' 
#' @details
#' \href{https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r115}{Horvath, S. DNA methylation age of human tissues and cell types. 
#' Genome Biol 14, 3156 (2013). https://doi.org/10.1186/gb-2013-14-10-r115}
#' @param x numeric vector of ages
#' @param adult_age Age of the adult of the species. From the original manuscript, 
#' 20 for humans and 15 for chimpanzees. 
#' @param inverse If TRUE, return transformed ages to the original scale
#' @return transformed ages
#' @export
#' @examples
#' 
#' age <- 0:100
#' transformed <- horvath_age(age)
#' plot(age, transformed, xlab="Age", ylab="Transformed Age", type="l")
#' 
#' # Conversion back to original scale
#' all.equal(age, horvath_age(transformed, inverse = TRUE))
horvath_age <- function(x, adult_age = 20, inverse = FALSE) {
  
  if (isTRUE(inverse)) {
    return(ifelse(x <= 0, 
                  exp(x) * (adult_age + 1) - 1, 
                  x * (adult_age + 1) + adult_age)
           )
  }
  
  ifelse(x <= adult_age, 
         log1p(x) - log1p(adult_age), 
         (x - adult_age) / (adult_age + 1)
  )
  
}