getDEGenes {MIGSA} | R Documentation

## 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

`igsaInput` | a valid IGSAinput object.

### 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);

[Package MIGSA version 1.8.1 Index]