PCAGenomicSignatures-methods {GenomicSuperSignature} | R Documentation

## Methods and accesors for `PCAGenomicSignatures` object

### Description

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

### Usage

    ## S4 replacement method for signature 'PCAGenomicSignatures'
    studies(x) <- value

    ## S4 replacement method for signature 'PCAGenomicSignatures'
    silhouetteWidth(x) <- value

    ## S4 replacement method for signature 'PCAGenomicSignatures'
    gsea(x) <- value

    ## S4 replacement method for signature 'PCAGenomicSignatures'
    trainingData(x) <- value

    ## S4 replacement method for signature 'PCAGenomicSignatures'
    mesh(x) <- value

    ## S4 replacement method for signature 'PCAGenomicSignatures'
    PCAsummary(x) <- value

    ## S4 method for signature 'PCAGenomicSignatures'
    studies(x)

    ## S4 method for signature 'PCAGenomicSignatures'
    silhouetteWidth(x)

    ## S4 method for signature 'PCAGenomicSignatures'
    gsea(x)

    ## S4 method for signature 'PCAGenomicSignatures'
    trainingData(x)

    ## S4 method for signature 'PCAGenomicSignatures'
    mesh(x)

    ## S4 method for signature 'PCAGenomicSignatures'
    PCAsummary(x)

    ## S4 method for signature 'PCAGenomicSignatures'
    show(object)

### Arguments

`value` | See details.
`object, x` | A `PCAGenomicSignatures` object

### Details

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

- metadata(x)$cluster : A vector of integers (from 1:k) indicating the cluster to which each PC is allocated.

- metadata(x)$size : The number of PCs in each cluster.

- metadata(x)$k : The number of RAVs.

- metadata(x)$n : The number of top PCs from each dataset.

- metadata(x)$geneSets : Name of the prior gene sets used to annotate average loadings.

- colData(x)$studies : A list of character vectors containing studies contributing to each PC cluster.

- colData(x)$gsea : A list of data frames. Each element is a subset of outputs from `clusterProfiler::GSEA` function.

### Value

PCAGenomicSignatures object with multiple setters or accessors

### Slots

`trainingData`

  A `DataFrame` class object for metadata associated with training data

### Setters

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

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

- studies<- : A list of character vectors containing gene sets used to annotate average loadings

- gsea<- : A list of `gseaResult` objects.

- metadata<- : A `list` object of metadata

- '$<-' : A vector to replace the indicated column in `colData`

### Accessors

All the accessors inherited from `SummarizedExperiment` are available and the additional accessors for `PCAGenomicSignatures` specific data are listed below.

- RAVindex : Equivalent to the `assay(x)`

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

- studies : Access the `colData(x)$studies` slot

- gsea : Access the `colData(x)$gsea`

- '$' : Access a column in `colData`

- trainingData : Access the `trainingData` slot

- mesh : Access the `trainingData(x)$MeSH` slot

- PCAsummary : Access the `trainingData(x)$PCAsummary` slot

### Examples

    data(miniRAVmodel)
    miniRAVmodel

[Package GenomicSuperSignature version 1.0.1 Index]