get_set_OmicsRegCateg: Access and Edit Response of an 'OmicsReg' or 'OmicsReg'...

In gabrielodom/pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Access and Edit Response of an OmicsReg or OmicsReg Object

Description

"Get" or "Set" the values of the response_num or response_fact slots of an object of class OmicsReg or OmicsReg, respectively.

Usage

getResponse(object, ...)

getResponse(object) <- value

## S4 method for signature 'OmicsPathway'
getResponse(object, ...)

## S4 replacement method for signature 'OmicsPathway'
getResponse(object) <- value

Arguments

object	An object of class OmicsReg-class or OmicsCateg-class.
...	Dots for additional internal arguments (currently unused).
value	The replacement object to be assigned to the response slot.

Details

These functions can be useful to set or extract the response vector from an object of class OmicsReg or OmicsReg. However, we recommend that users simply create a new, valid object instead of modifying an existing one. The validity of edited objects is checked with their respective ValidOmicsCateg or ValidOmicsReg function. Because both classes have a response slot, we set this method for the parent class, OmicsPathway-class.

Value

The "get" functions return the objects in the slots specified: getResponse returns the response_num vector from objects of class OmicsReg and the response_fact vector from objects of class OmicsCateg. These functions can extract these values from any valid object of those classes.

The "set" functions enable the user to edit or replace the object in the response_num slot for any OmicsReg object or response_fact slot for any OmicsCateg object, provided that the new values do not violate the validity check of such an object. See "Details" for more information.

See Also

CreateOmics

Examples

  data("colonSurv_df")
  data("colon_pathwayCollection")

  colon_Omics <- CreateOmics(
    assayData_df = colonSurv_df[, -(2:3)],
    pathwayCollection_ls = colon_pathwayCollection,
    response = colonSurv_df[, c(1, 2)],
    respType = "reg"
  )

  getResponse(colon_Omics)

gabrielodom/pathwayPCA documentation built on July 10, 2023, 3:32 a.m.