useDynLib("Ringo", ringoSlidingQuantile=sliding_quantile, ringoRegionOverlap=overlap_xy, ringoMovingMeanSd=moving_mean_sd)

import("methods")
import("graphics") 

export("autocor", "chipAlongChrom","corPlot", "whichCsr",
       "computeRunningMedians", "sliding.quantile",
       "findChersOnSmoothed", "cherByThreshold","newCher","relateChers",
       "preprocess","nimblegenScale","readNimblegen", "asExprSet",
       "as.data.frame.cherList","ftr2xys","compute.gc",
       "posToProbeAnno","validProbeAnno", "regionOverlap",
       "features2Probes","sliding.meansd", "computeSlidingT",
       "getFeats", "upperBoundNull")

S3method("plot", "autocor.result")
S3method("image", "RGList")
S3method("as.data.frame", "cherList")

exportClasses("probeAnno", "cher")

exportMethods("get", "ls","initialize", "plot", "show",
              "arrayName", "chromosomeNames", "genome",
              "arrayName<-", "genome<-", "update",
              "cellType", "cellType<-")
