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

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

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/PCAGenomicSignatures documentation built on May 3, 2023, 11:21 a.m.