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

GenomicSignatures-methodsR 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 method for signature 'GenomicSignatures'
version(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

  • version : Access the metadata(x)$version slot

Examples

data(miniRAVmodel)
miniRAVmodel



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