R/anota2seqClasses.R

In anota2seq: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

## anota2seq S4 class implementation
setClassUnion("listOrNULL",members=c("list", "NULL"))
setClassUnion("numOrNULL",members =c("numeric","NULL"))
setClassUnion("batchVec",members=c("numeric","character","NULL"))
setClassUnion("matrixOrNULL",members = c("matrix","NULL"))
setClass("Anota2seqQualityControl",
         slots = c(
             omniIntStats = "matrix",
             omniGroupStats = "matrix",
             groupIntercepts = "matrix",
             correctionMethod = "character",
             dsfSummary = "numeric",
             dfbetas = "matrix",
             residuals = "matrix",
             fittedValues = "matrix",
             phenoClasses = "character",
             sampleNames = "character",
             abParametersInt = "numOrNULL",
             abParametersGroup = "numOrNULL"
         ))
setClass("Anota2seqResidOutlierTest",
         slots = c(
             confInt = "numeric",
             inputResiduals = "matrix",
             rnormIter = "numeric",
             outlierMatrixLog = "matrix",
             meanOutlierPerIteration = "numeric",
             obtainedComparedToExpected = "numeric",
             nExpected = "numeric",
             nObtained= "numeric"
         ))
## Class that holds the standard output of the anota2seqAnalyse function (slightly reduced to avoid redundancy)
setClass("Anota2seqOutput",
         slots=c(
             apvStats = "listOrNULL",
             apvStatsRvm = "listOrNULL",
             correctionMethod = "character",
             usedContrasts = "matrix",  
             abList = "list"
         ))
## Class that holds the output of anota2seqSelectSignificantGenes 
setClass("Anota2seqSelectedOutput",
         slots= c(
             selectedData = "listOrNULL",
             selectedRvmData = "listOrNULL",
             useRVM = "logical",
             deltaData = "listOrNULL",
             usedThresholds = "listOrNULL"
         ))
setClass("Anota2seqMRNAabundanceOutput",
         slots = c(
             totalmRNA = "listOrNULL",
             translatedmRNA = "listOrNULL",
             useRVM = "logical",
             mRNASelect = "logical"
         ))
setClassUnion("qcOrNULL",members = c("Anota2seqQualityControl", "NULL"))
setClassUnion("residOrNULL", members = c("Anota2seqResidOutlierTest", "NULL"))
setClassUnion("outOrNULL", members = c("Anota2seqOutput", "NULL"))
setClassUnion("selOutOrNULL", members = c("Anota2seqSelectedOutput", "NULL"))
setClassUnion("abundOrNULL", members =  c("Anota2seqMRNAabundanceOutput", "NULL"))
setClass("Anota2seqDataSet",
         slots = c(
             dataT = "matrix",
             dataP = "matrix",
             phenoVec = "character",
             batchVec = "batchVec",
             contrasts = "matrixOrNULL",
             qualityControl = "qcOrNULL",
             residOutlierTest = "residOrNULL",
             translatedmRNA = "outOrNULL",
             totalmRNA = "outOrNULL",
             translation = "outOrNULL",
             buffering = "outOrNULL",
             selectedTranslatedmRNA="selOutOrNULL",
             selectedTotalmRNA = "selOutOrNULL",
             selectedTranslation = "selOutOrNULL",
             selectedBuffering = "selOutOrNULL",
             mRNAAbundance = "abundOrNULL",
             deltaData = "listOrNULL",
             regModes = "logical"
         ))