Calculate differentialy expressed genes of an IGSAinput object

Description

getDEGenes calculates the differentialy expressed genes of an IGSAinput object using the expression matrix, the FitOtions and the SEAparams..

Usage

getDEGenes(igsaInput)

## S4 method for signature 'IGSAinput'
getDEGenes(igsaInput)

Arguments

Value

A IGSAinput object with the updated slots and DE genes calculated.

See Also

IGSAinput-class

Examples

## Lets create a basic IGSAinput object.
## First create a expression matrix.
maData <- matrix(rnorm(10000),ncol=4);
rownames(maData) <- 1:nrow(maData); # It must have rownames (gene names).
maExprData <- new("MAList",list(M=maData));

## Now lets create the FitOptions object.
myFOpts <- FitOptions(c("Cond1", "Cond1", "Cond2", "Cond2"));

## Lets create our IGSAinput object.
myIgsaInput <- IGSAinput(name="myIgsaInput", expr_data=maExprData, 
fit_options=myFOpts);

## And check how many differentialy expressed genes does it get with actual
## parameters.
aux <- getDEGenes(myIgsaInput);