get_set_OmicsPathway: Access and Edit Assay or 'pathwayCollection' Values in...

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

Access and Edit Assay or pathwayCollection Values in Omics* Objects

Description

"Get" or "Set" the values of the assayData_df, sampleIDs_char, or pathwayCollection slots of an object of class OmicsPathway or a class that extends this class (OmicsSurv, OmicsReg, or OmicsCateg).

Usage

getAssay(object, ...)

getAssay(object) <- value

getSampleIDs(object, ...)

getSampleIDs(object) <- value

getPathwayCollection(object, ...)

getPathwayCollection(object) <- value

getTrimPathwayCollection(object, ...)

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

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

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

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

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

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

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

Arguments

object	An object of or extending OmicsPathway-class: that class, OmicsSurv-class, OmicsReg-class, or OmicsCateg-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 assay data or pathways list from an Omics*-class object. However, we recommend that users simply create a new, valid Omics* object instead of modifying an existing one. The validity of edited objects is checked with the ValidOmicsSurv, ValidOmicsCateg, or ValidOmicsReg functions.

Further, because the pathwayPCA methods require a cleaned (trimmed) pathway collection, the trimPathwayCollection slot is read-only. Users may only edit this slot by updating the pathway collection provided to the pathwayCollection slot. Despite this functionality, we strongly recommend that users create a new object with the updated pathway collection, rather than attempting to overwrite the slots within an existing object. See IntersectOmicsPwyCollct for details on trimmed pathway collection.

Value

The "get" functions return the objects in the slots specified: getAssay returns the assayData_df data frame object, getSampleIDs returns the sampleIDs_char character vector, getPathwayCollection returns the pathwayCollection list object, and getTrimPathwayCollection returns the trimPathwayCollection. These functions can extract these values from any valid OmicsPathway, OmicsSurv, OmicsReg, or OmicsCateg object.

The "set" functions enable the user to edit or replace objects in the assayData_df, sampleIDs_char, or pathwayCollection slots for any OmicsPathway, OmicsSurv, OmicsReg, or OmicsCateg objects, provided that the new values do not violate the validity checks of their respective objects. Because the slot for trimPathwayCollection is filled upon object creation, and to ensure that this pathway collection is "clean", there is no "set" function for the trimmed pathway collection slot. Instead, users can update the pathway collection, and the trimmed pathway collection will be updated automatically. See "Details" for more information on the "set" functions.

See Also

CreateOmics

Examples

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

  colon_Omics <- CreateOmics(
    assayData_df = colonSurv_df[, -(2:3)],
    pathwayCollection_ls = colon_pathwayCollection
  )

  getAssay(colon_Omics)
  getPathwayCollection(colon_Omics)

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