get_set_OmicsSurv: Access and Edit Event Time or Indicator in an 'OmicsSurv'...

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

Description

"Get" or "Set" the values of the eventTime_num or eventObserved_lgl slots of an object of class OmicsSurv.

Usage

getEventTime(object, ...)

getEventTime(object) <- value

getEvent(object, ...)

getEvent(object) <- value

## S4 method for signature 'OmicsSurv'
getEventTime(object, ...)

## S4 replacement method for signature 'OmicsSurv'
getEventTime(object) <- value

## S4 method for signature 'OmicsSurv'
getEvent(object, ...)

## S4 replacement method for signature 'OmicsSurv'
getEvent(object) <- value

Arguments

object	An object of class OmicsSurv-class.
...	Dots for additional internal arguments (currently unused).
value	The replacement object to be assigned to the specified slot.

Details

These functions can be useful to set or extract the event time or death indicator from an OmicsSurv object. However, we recommend that users simply create a new, valid OmicsSurv object instead of modifying an existing one. The validity of edited objects is checked with the ValidOmicsSurv function.

Value

The "get" functions return the objects in the slots specified: getEventTime returns the eventTime_num vector object and getEvent returns the eventObserved_lgl vector object. These functions can extract these values from any valid OmicsSurv object.

The "set" functions enable the user to edit or replace objects in the eventTime_num or eventObserved_lgl slots for any OmicsSurv object, provided that the new values do not violate the validity check of an OmicsSurv 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[, 1:3],
    respType = "survival"
  )

  getEventTime(colon_Omics)
  getEvent(colon_Omics)

pathwayPCA documentation built on Dec. 15, 2020, 6:14 p.m.