plot.STP {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 Single Time Point Analysis for detecting differentially expressed genes in gene expression data.
## S3 method for class 'STP' plot(x, FDR=TRUE, AC=TRUE, WARNINGS=FALSE, tp=NULL, ...)
x |
an object of class ' |
FDR |
if |
AC |
if |
WARNINGS |
if |
tp |
a character string to be added at the end of the plot's title
(used for adding time points in |
... |
further arguments passed to or from other methods. |
Juan Pablo Acosta (jpacostar@unal.edu.co).
## Single time point analysis for 500 genes with 10 treatment ## replicates and 10 control replicates n <- 500; p <- 20; p1 <- 10 des <- c(rep(1, p1), rep(2, (p-p1))) mu <- as.matrix(rexp(n, rate=1)) Z <- t(apply(mu, 1, function(mui) rnorm(p, mean=mui, sd=1))) ### 5 up regulated genes Z[1:5,1:p1] <- Z[1:5,1:p1] + 5 ### 10 down regulated genes Z[6:15,(p1+1):p] <- Z[6:15,(p1+1):p] + 4 resSTP <- stp(Z, des) resSTP plot(resSTP)