miage: Estimate mitotic age from DNAm using the MiAge algorithm

In perishky/meffonym: DNA methylation exposure and phenotypic archive

Estimate mitotic age from DNAm using the MiAge algorithm

Description

Define the following: * x[i,j] be the methylation level of CpG site i in sample j * E(X[n,i]) be the expected methylation level of CpG site i after n generations, * a[i] be the rate of de novo methylation of CpG site i * b[i] be the fidelity of methylation maintenance of CpG site i * c[i] = a[i]/(1-b[i]) * d[i] = E(X[1,i]) - c[i]

Usage

miage(
  x,
  b = NULL,
  c = NULL,
  d = NULL,
  minage = 10,
  maxage = 10000,
  inits = c(500, minage + (1:4) * (maxage - minage)/5)
)

Arguments

x	DNA methylation matrix (rows=CpG sites, columns=samples). Missing values in x will be replaced with the mean value of the row.
b	As defined above (Default: published values).
c	As defined above (Default: published values).
d	As defined above (Default: published values).
minage	Lowest age to consider (Default: 10).
maxage	Highest age to consider (Default: 10000).
inits	Initial ages to consider at each iteration. (Default: 500 and lowerage + (1:4)*(maxage-minage)/5).

Details

This function estimates the number of generations n[j] for each sample j from the DNA methylation levels x[,j] of 268 CpG sites. The estimate is obtained by selecting the value n[j] that minimizes the sum of (E(X[n,i])-x[i,j])^2 across CpG sites i=1..268 where E(X[n,i]) is estimated as c[i] + b[i]^(n[j]-1)*d[i] for given b[i], c[i] and d[i].

Value

Estimated mitotic age for each sample.

perishky/meffonym documentation built on Nov. 8, 2024, 8:36 p.m.