IGSAinput-getDEGenes: Calculate differentialy expressed genes of an IGSAinput...
In MIGSA: Massive and Integrative Gene Set Analysis

Description Usage Arguments Value See Also Examples

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

getDEGenes(igsaInput)

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

igsaInput

a valid IGSAinput object.

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

IGSAinput-class

## 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)