acde (version 1.2.0)

plot.STP: Plot Method for Single Time Point Analysis

Description

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.

Usage

"plot"(x, FDR=TRUE, AC=TRUE, WARNINGS=FALSE, tp=NULL, ...)

Arguments

x

an object of class 'STP' as returned by function stp.

FDR

if TRUE, a plot of the estimated FDR is displayed.

AC

if TRUE, a plot of the differentially expressed genes in the artificial components is displayed.

WARNINGS

if TRUE and if a BCa confidence upper bound was computed for obtaining x, the threshold values for which an extreme order statistic was used in the BCa computations are shown (these warnings are produced in calls to boot.ci).

tp

a character string to be added at the end of the plot's title (used for adding time points in plot.TC).

...

further arguments passed to or from other methods.

See Also

stp, print.STP.

Examples

## 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)