IGSAinput-getterSetters: Accessors for IGSAinput class

In MIGSA: Massive and Integrative Gene Set Analysis

Description

Getters and setters functions to access IGSAinput object slots.

Usage

`IGSAinput-getterSetters`(object)

name(object)

## S4 method for signature 'IGSAinput'
name(object)

name(object) <- value

## S4 replacement method for signature 'IGSAinput'
name(object) <- value

fitOptions(object)

## S4 method for signature 'IGSAinput'
fitOptions(object)

fitOptions(object) <- value

## S4 replacement method for signature 'IGSAinput'
fitOptions(object) <- value

exprData(object)

## S4 method for signature 'IGSAinput'
exprData(object)

exprData(object) <- value

## S4 replacement method for signature 'IGSAinput'
exprData(object) <- value

geneSetsList(object)

## S4 method for signature 'IGSAinput'
geneSetsList(object)

geneSetsList(object) <- value

## S4 replacement method for signature 'IGSAinput'
geneSetsList(object) <- value

gseaParams(object)

## S4 method for signature 'IGSAinput'
gseaParams(object)

gseaParams(object) <- value

## S4 replacement method for signature 'IGSAinput'
gseaParams(object) <- value

seaParams(object)

## S4 method for signature 'IGSAinput'
seaParams(object)

seaParams(object) <- value

## S4 replacement method for signature 'IGSAinput'
seaParams(object) <- value

Arguments

object	IGSAinput object.
value	value to replace in the slot.

Value

Modified IGSAinput object or desired slot.

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"))
## And now we can create our IGSAinput ready for MIGSA.
igsaInput <- IGSAinput(
  name = "igsaInput", expr_data = maExprData,
  fit_options = myFOpts
)
## Lets get igsaInput values, and modify its name.
name(igsaInput)
name(igsaInput) <- "newName"
fitOptions(igsaInput)
exprData(igsaInput)
geneSetsList(igsaInput)
gseaParams(igsaInput)
seaParams(igsaInput)

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.