SubsetOmicsPath {pathwayPCA} | R Documentation

## 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)

[Package pathwayPCA version 1.6.3 Index]