IGSAinput-getDEGenes: Calculate differentialy expressed genes of an IGSAinput...

In jcrodriguez1989/MIGSA: Massive and Integrative Gene Set Analysis

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)

jcrodriguez1989/MIGSA documentation built on Nov. 1, 2020, 8:04 a.m.