plot.STP {acde} | R Documentation

## 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

    ## S3 method for class 'STP'
    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.

### Author(s)

Juan Pablo Acosta (jpacostar@unal.edu.co).

### 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)

[Package acde version 1.12.0 Index]