print.STP: Print Method for Single Time Point Analysis

In acde: Artificial Components Detection of Differentially Expressed Genes

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)

acde documentation built on Nov. 8, 2020, 11:10 p.m.