R/AllClasses.r

In Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

setClass("Data4Cseq",
    representation=list( 
        viewpointChromosome="character",
        viewpointInterval="numeric",
        readLength="numeric",
        pointsOfInterest="data.frame",
        rawReads="GAlignments",
        rawFragments="data.frame",
        nearCisFragments="data.frame"
    ),

    prototype=prototype(
        viewpointChromosome="chr1",
        viewpointInterval=c(1,2),
        readLength=30,
        pointsOfInterest=data.frame(),
        rawReads=GAlignments(),
        rawFragments=data.frame(),
        nearCisFragments=data.frame()
    ),

    validity=function(object) {
        if (length(readLength(object)) != 1)
            return("Read length has to be a single number")
        if (length(viewpointInterval(object)) != 2)
            return("The viewpoint interval should consist of a start and end coordinate of the form c(A, B)")
        return(TRUE)
    }
)