R/AllClasses.R

In MAIT: Statistical Analysis of Metabolomic Data

setClass("MAIT.Parameters",
         representation(
                        sampleProcessing="list",
                        peakAnnotation="list",
                        peakAggregation="list",
                        sigFeatures="list",
                        biotransformations="list",
                        identifyMetabolites="list",
                        classification="list",
                        plotPCA="list",
                        plotPLS="list",
                        plotHeatmap="list"
                        ),
         prototype(
                        sampleProcessing=list(),
                        peakAnnotation=list(),
                        peakAggregation=list(),
                        sigFeatures=list(),
                        biotransformations=list(),
                        identifyMetabolites=list(),
                        classification=list(),
                        plotPCA=list(),
                        plotPLS=list(),
                        plotHeatmap=list()
			)
         );


setClass("MAIT.FeatureData",
         representation(
                        scores="matrix",
                        featureID="vector",
                        featureSigID="vector",
                        LSDResults="matrix",
                        models="list",
                        pvalues="vector",
			pvaluesCorrection="character",
                        pcaModel="list",
                        plsModel="list",
                        masses="numeric",
                        rt="numeric",
                        extendedTable="data.frame"
                        ),
         prototype(
                        scores=matrix(),
                        featureID=vector(),
                        featureSigID=vector(),
                        LSDResults=matrix(),
                        models=list(),
                        pvalues=vector(),
			pvaluesCorrection="",
                        pcaModel=list(),
                        plsModel=list(),
                        masses=numeric(),
                        rt=numeric(),
                        extendedTable=data.frame()
			)
         );

setClass("MAIT.FeatureInfo",
         representation(
                        biotransformations="matrix",
                        peakAgMethod="character",
                        metaboliteTable="data.frame"
                        ),
         prototype(
                        biotransformations=matrix(),
                        peakAgMethod="",
                        metaboliteTable=data.frame())
         );

setClass("MAIT.PhenoData",
         representation(
                        classes="vector",
                        classNum="vector",
			resultsPath="character"
                        ),
         prototype(
                        classes=vector(),
                        classNum=vector(),
			resultsPath=""
			)
         );

setClass("MAIT.RawData",
         representation(
                        parameters="MAIT.Parameters",
                        data="list"                       
                        ),
         prototype(
                        parameters=new("MAIT.Parameters"),
                        data=list()         
			)
         );

setClass("MAIT.Validation",
         representation(
                        ovClassifRatioTable="matrix",
                        ovClassifRatioData="list",
                        classifRatioClasses="matrix"                       
                        ),
         prototype(
                        ovClassifRatioTable=matrix(),
                        ovClassifRatioData=list(),
                        classifRatioClasses=matrix()
			)
         );

setClass("MAIT",
         representation(
                        FeatureInfo="MAIT.FeatureInfo",
                        RawData="MAIT.RawData",
                        Validation="MAIT.Validation",
                        PhenoData="MAIT.PhenoData",
                        FeatureData="MAIT.FeatureData"
                        ),
         prototype(
                        FeatureInfo=new("MAIT.FeatureInfo"),
                        RawData=new("MAIT.RawData"),
                        Validation=new("MAIT.Validation"),
                        PhenoData=new("MAIT.PhenoData"),
                        FeatureData=new("MAIT.FeatureData"))
         );