getDEGenes {MIGSA} | R Documentation |
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.
## 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)