Difference between revisions of "GGBsnippet.R"

Latest revision as of 00:38, 6 June 2007

Code snipits and programs written in R, S or S-PLUS

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"

a.shape <- params[1] a0.shape <- params[2] scale <- params[3]

DEscales <- rgamma(2*m1, shape=a0.shape, rate=scale) EEscales <- rgamma(m0 , shape=a0.shape, rate=scale)

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)

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))

@@ Line 1: / Line 1: @@
-p <- 1000
+# {{R}}
-n <- 10
+# p (genes) by n (slides) matrix
-a.shape  <- parameters[1]
+# m=p keeping fdr notation
-a0.shape <- parameters[2]
-scale    <-   parameters[3]
+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"
+a.shape  <- params[1]
+a0.shape <- params[2]
+scale    <- params[3]
 DEscales <- rgamma(2*m1, shape=a0.shape, rate=scale)
 EEscales <- rgamma(m0 , shape=a0.shape, rate=scale)
-scales   <- c(rep(DEscales, each=slides), rep(EEscales, each=2*slides)) # same as p
+scales   <- c(rep(DEscales, each=nreps), rep(EEscales, each=2*nreps))
 X <- rgamma(n* p, a.shape, rate=scales)
-dim(X) <- c(p, n)
+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))