MBAmethyl-package {MBAmethyl}

R Documentation

Model-based analysis of DNA methylation data

Description

This package provides functions for reconstructing DNA methylation values from raw measurements. It utilize both the information from biological replicates and neighboring probes by explicitly modeling the probe-specific effect and encouraging the neighboring similarity by a group fused lasso penalty.

Details

Package:	MBAmethyl
Type:	Package
Version:	0.99.0
Date:	2014-08-24
License:	Artistic-2.0

Author(s)

Tao Wang, Mengjie Chen

Maintainer: Tao Wang <tao.wang.tw376@yale.edu>

References

~~ Literature or other references for background information ~~

Examples

 p <- 80
  n <- 40
  K <- 2
  k <- K - 1
  cp <- numeric()
  L <- c(0, floor(p / K) * (1 : k), p)
  cp <- floor(p / K) * (1 : k) + 1

  ## phi0: probe effects; theta0: true methylation values; part: partition of probe indices
  phi0 <- runif(p, 0.5, 2.0)
  theta0 <- matrix(0, p, n)
  part <- list()

  for (s in 1 : K) {
    part[[s]] <- (L[s] + 1) : L[s + 1]
    phi0[part[[s]]] <- phi0[part[[s]]] / sqrt(mean(phi0[part[[s]]]^2))
  }

  theta0[part[[1]], ] <- rep(1, length(part[[1]])) 
  theta0[part[[2]], ] <- rep(1, length(part[[2]])) 
  
  error <- matrix(runif(p * n, 0, 0.1), p, n)
  Y <- theta0 * phi0  + error
  fit <- MBAmethyl(Y, steps = 10)

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