# Dependencies
import(methods)
import(Rgb)
importFrom(DNAcopy, "CNA", "smooth.CNA", "segment")

# Constructors
export("cghRA.design", "Agilent.design", "custom.design")
export("cghRA.probes", "Agilent.probes", "custom.probes")
export("cghRA.regions")
export("cghRA.copies")
export("cghRA.series")
export("cghRA.array")

# Classes
exportClasses("cghRA.design")
exportClasses("cghRA.probes")
exportClasses("cghRA.regions")
exportClasses("cghRA.copies")
exportClasses("cghRA.series")
exportClasses("cghRA.array")

# Process
export("process")
exportPattern("^process\\.")

# Interface
export("tk.cghRA")
export("tk.design")
export("tk.process")
export("tk.modelize", "tk.value")
export("tk.annotate")
export("tk.series")

# cghRA functions
export("parseKaryo")

# cghRA.probes functions
export("blatInstall")
export("localize")
export("bias")
export("WACA")

# cghRA.regions functions
export("STEPS", "SRA", "LRA")
export("parallelize")
export("penetrance")
export("fillGaps")
export("GEDI")

# cghRA.copies functions
export("model.auto")
export("model.test")
export("model.apply")
export("copies")
export("LCN")

# cnvScore functions
export("cnvScore")
export("map2design")
export("applyMap")
export("trace2track")
export("track.CNV.DGVsupp")

# Rgb integration
export("drawableFromClass.cghRA.probes")

