fixAge: Turn 'epigenetic clock' into actual age

In trichelab/biscuitEater: Convenience Functions for Biscuit

Turn 'epigenetic clock' into actual age

Description

Uses Horvath-type 'epigenetic clock' raw output to project into actual ages

Usage

fixAge(x, adult = 21)

Arguments

x	Untransformed or raw prediction(s)
adult	Age of adulthood (DEFAULT: 21)

Details

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.

Value

  Transformed prediction(s)

Examples

  clock <- getClock(genome="hg38")
  score <- clock$gr$score

  age <- fixAge(score)

trichelab/biscuitEater documentation built on March 2, 2024, 6:57 p.m.