MBAmethyl-package {MBAmethyl} | R Documentation |
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.
Package: | MBAmethyl |
Type: | Package |
Version: | 0.99.0 |
Date: | 2014-08-24 |
License: | Artistic-2.0 |
Tao Wang, Mengjie Chen
Maintainer: Tao Wang <tao.wang.tw376@yale.edu>
~~ Literature or other references for background information ~~
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)