plot.TC {acde} | R Documentation |
a method for the plot generic. It is designed for displaying plots of the estimated FDR and the genes' classification when performing a Time Course Analysis for detecting differentially expressed genes in gene expression data.
## S3 method for class 'TC' plot(x, iRatios=TRUE, FDR = TRUE, AC = TRUE, WARNINGS = FALSE, ...)
x |
if |
iRatios |
an object of class ' |
FDR |
if |
AC |
if |
WARNINGS |
if |
... |
further arguments passed to or from other methods. |
Juan Pablo Acosta (jpacostar@unal.edu.co).
tc
, print.TC
, summary.TC
.
## Time course analysis for 500 genes with 10 treatment ## replicates and 10 control replicates tPts <- c("h0", "12h", "24h") n <- 500; p <- 20; p1 <- 10 Z <- vector("list", 3) des <- vector("list", 3) for(tp in 1:3){ des[[tp]] <- c(rep(1, p1), rep(2, (p-p1))) } mu <- as.matrix(rexp(n, rate=1)) ### h0 time point (no diff. expr.) Z[[1]] <- t(apply(mu, 1, function(mui) rnorm(p, mean=mui, sd=1))) ### h12 time point (diff. expr. begins) Z[[2]] <- t(apply(mu, 1, function(mui) rnorm(p, mean=mui, sd=1))) #### Up regulated genes Z[[2]][1:5,1:p1] <- Z[[2]][1:5,1:p1] + matrix(runif(5*p1, 1, 3), nrow=5) #### Down regulated genes Z[[2]][6:15,(p1+1):p] <- Z[[2]][6:15,(p1+1):p] + matrix(runif(10*(p-p1), 1, 2), nrow=10) ### h24 time point (maximum differential expression) Z[[3]] <- t(apply(mu, 1, function(mui) rnorm(p, mean=mui, sd=1))) #### 5 up regulated genes Z[[3]][1:5,1:p1] <- Z[[3]][1:5,1:p1] + 5 #### 10 down regulated genes Z[[3]][6:15,(p1+1):p] <- Z[[3]][6:15,(p1+1):p] + 4 resTC <- tc(Z, des) resTC summary(resTC) plot(resTC) ## Not run: ## Phytophthora Infestans Time Course Analysis (takes time...) dataPI <- phytophthora desPI <- vector("list", 4) for(tp in 1:4){ desPI[[tp]] <- c(rep(1, 8), rep(2, 8)) } resPI <- tc(dataPI, desPI) resPI summary(resPI) plot(resPI) ## End(Not run)