useDynLib("tilingArray")

importFrom("graphics", "plot")
importFrom("methods", "show")
importFrom("stats", "confint")
importFrom("stats", "logLik")

export("normalizeByReference", "segment", "costMatrix", 
       "findSegments", ## this is for backward compatibility, should be deprecated
       "sampleStep", "readCel2eSet",
       "posMin", "otherStrand",
       "plotAlongChrom", "comparisonPlot")


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

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

