PCAGenomicSignatures-methods: Methods and accesors for 'PCAGenomicSignatures' object

In shbrief/GenomicSuperSignature: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

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

shbrief/GenomicSuperSignature documentation built on May 3, 2023, 10:07 p.m.