GenomicSignatures-methods {GenomicSuperSignature} | R Documentation

## Methods and accesors for `GenomicSignatures` object

### Description

The default contents of `GenomicSignatures` object, with a set of getter and setter generic functions, which extract either the `assay`, `colData`, or `metadata` slots of a `GenomicSignatures-class` object. When you create this object, `colData$studies` should be populated before adding any information in `trainingData` slot.

### Usage

    ## S4 method for signature 'GenomicSignatures'
    RAVindex(x)

    ## S4 method for signature 'GenomicSignatures'
    geneSets(x)

    ## S4 method for signature 'GenomicSignatures'
    updateNote(x)

    ## S4 replacement method for signature 'GenomicSignatures'
    geneSets(x) <- value

    ## S4 replacement method for signature 'GenomicSignatures'
    updateNote(x) <- value

### Arguments

`x` | A `GenomicSignatures` object
`value` | See details.

### Details

- assay(x) : RAVindex (= avgLoadings) containing genes x RAVs

- metadata(x) : Metadata associated with RAVindex building process

- colData(x) : Information on RAVs

### Value

A GenomicSignatures object for the constructor

### Setters

Setter method values (i.e., `function(x) <- value`):

- metadata<- : Assign metadata

- coldata<- : Assign extra information associated with RAVs

- geneSets<- : A character vector containing the name of gene sets used to annotate average loadings

- updateNote<- : A character vector. Describes the main feature of a model construction

### Getters

- RAVindex : Equivalent to `assays(x)$RAVindex`

- geneSets : Access the `metadata(x)$geneSets` slot

- updateNote : Access the `metadata(x)$updateNote` slot

### Examples

    data(miniRAVmodel)
    miniRAVmodel

[Package GenomicSuperSignature version 1.2.1 Index]