R/AllClasses.R

In dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

# Dpeak data class

setClass( Class="DpeakData",
    representation=representation(
        fragSet="list",

        PET="logical",
        fragLenTable="table",
        Fratio="numeric",
        aveFragLen="numeric",

        stackedFragment="list",

        peakChr="character",
        peakStart="numeric",
        peakEnd="numeric",

        emptyList="character"
    )
)

# Dpeak motif class

setClass( Class="DpeakMotif",
    representation=representation(
        motif="character",
        locMotif="list",

        peakChr="character",
        peakStart="numeric",
        peakEnd="numeric"
    )
)

# Dpeak fit class

setClass( Class="DpeakFit",
    representation=representation(
        fits="list",

        optFit="list",
        optMu="list",
        optPi="list",
        optPi0="list",
        optGamma="list",
        optDelta="list",
        optSigma="list",
        bicVec="list",
        aicVec="list",

        fragSet="list",
        PET="logical",
        fragLenTable="table",
        Fratio="numeric",
        aveFragLen="numeric",

        stackedFragment="list",

        peakChr="character",
        peakStart="numeric",
        peakEnd="numeric",

        estDeltaSigma="character",
		    nTop="numeric",
        lbDelta="numeric",
        lbSigma="numeric",
        psize="numeric",
        maxComp="numeric",
        pConst="numeric",
        iterInit="numeric",
        iterMain="numeric",
        epsilon="numeric"
    )
)