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 1.12.0 Index]