useDynLib("tilingArray")

import("methods")
import("grid")
importFrom("stats4", "plot")
importFrom("stats", "confint", "logLik", "residuals")
importFrom("strucchange", "breakpoints")
importFrom("vsn", "vsnMatrix")
importFrom("RColorBrewer", "brewer.pal")
importFrom("genefilter", "shorth")
importFrom("affy", "ReadAffy", "intensity")

export("normalizeByReference", "segment", "costMatrix", 
       "findSegments", ## this is for backward compatibility, should be deprecated
       "sampleStep", "readCel2eSet",
       "posMin", "otherStrand",
       "plotAlongChrom", "plotAlongChromLegend", "plotSegmentationHeatmap",
       "plotSegmentationDots", "plotFeatures", "comparisonPlot", "plotPenLL",
       "qcPlots", "PMindex", "BGindex", "segChrom")

S3method("residuals", "breakpointsPretend")
S3method("breakpoints", "breakpointsPretend")

export("residuals.breakpointsPretend",
       "breakpoints.breakpointsPretend")
       
exportClasses("segmentation")
exportMethods("plot", "show", "confint", "logLik")

