print.STP {acde} | R Documentation

## Print Method for Single Time Point Analysis

### Description

a method for the print generic. It prints relevant results when performing a Single Time Point Analysis for detecting differentially expressed genes in gene expression data.

### Usage

    ## S3 method for class 'STP'
    print(x, headerSTP = TRUE, ...)

### Arguments

`x` | an object of class '`STP`' as returned by function `stp`.
`headerSTP` | if `FALSE`, the header is omitted (used for `print.TC`).
`...` | further arguments passed to or from other methods.

### Details

If the desired FDR level was achieved (i.e. `x$astar <= x$alpha`), the results are printed for the differentially expressed genes and 10 more rows only. If the desired FDR level was not achieved, only ten rows are displayed.

### See Also

`stp`, `plot.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]