GGB-correlation-snippet.R
Code snipits and programs written in R, S or S-PLUS
- p (genes) by n (slides) matrix
- m=p keeping fdr notation
m <- p <- 1000 nreps <- 5
n <- nreps * 2 pi0 <- 0.95
m1 <- round(m * (1-pi0)) m0 <- p - m1
params <- c(2.74886, 1.36546, 4.12844) # "IPTG-a parameters" k <- 1000
a.shape <- params[1] a0.shape <- params[2] scale <- params[3]
kDE <- rgamma(2*m1, shape=k, rate=k) # p49 2001 NEWTON paper DEscales <- rgamma(2*m1, shape=a0.shape, rate=scale) DEscales <- DEscales * kDE
kEE <- rgamma(m0, shape=k, rate=k) EEscales <- rgamma(m0 , shape=a0.shape, rate=scale) EEscales <- EEscales / kEE
scales <- c(rep(DEscales, each=nreps), rep(EEscales, each=2*nreps)) X <- rgamma(n* p, a.shape, rate=scales) dim(X) <- c(n,p)
X <- t(X)
- Graphical check
hist(kDE, prob=TRUE) lines(density(kDE))
hist(kEE, prob=TRUE) lines(density(kEE))
Xbar <- rowMeans(log2(X)) hist(Xbar, breaks=30, prob=TRUE) lines(density(Xbar)) pairs(log2(X))
