R/chooseNearCisFragments.r

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

.chooseNearCisFragments <- function(expData, regionCoordinates, deleteViewpoint = TRUE) {

    fragmentData = rawFragments(expData)

    # for cis-interactions: only consider viewpoint chromosome
    fragmentData <- subset(fragmentData, fragmentData$chromosomeName == viewpointChromosome(expData))

    # delete viewpoint fragments, if chosen (default: TRUE)
    if (deleteViewpoint) {
        fragmentData = subset(fragmentData, (fragmentData$fragmentEnd < viewpointInterval(expData)[1] | fragmentData$fragmentStart > viewpointInterval(expData)[2]))
    }

    # pick relevant fragments for visualization range
    relevantFragments = (subset(fragmentData, (fragmentData$fragmentStart >= regionCoordinates[1] & fragmentData$fragmentEnd <= regionCoordinates[2])))

    return(relevantFragments)  
}




setMethod("chooseNearCisFragments",
    signature=signature(expData="Data4Cseq", regionCoordinates="numeric"),
    .chooseNearCisFragments)