useDynLib("vsn")

import("Biobase")
import("ggplot2")

importFrom("grDevices", "colorRampPalette")
importFrom("graphics", "matplot")
importFrom("methods", ".valueClassTest", "as", "is", "new", "slot", "validObject", "show")
importFrom("stats", "df", "median", "quantile", "rgamma", "rnorm", "runif", "predict", "logLik",
           "coef", "coefficients")
importFrom("lattice", "levelplot")
importFrom("affy", "rma", "normalize.AffyBatch.methods", "upDate.normalize.AffyBatch.methods",
           "indexProbes", "intensity", "intensity<-")

importClassesFrom("limma", "RGList")
importClassesFrom("affy", "AffyBatch")

exportClasses("vsn", "vsnInput")

export("vsnMatrix", "justvsn", "vsnrma", "sagmbAssess", "sagmbSimulateData",
       "plotVsnLogLik", "scalingFactorTransformation")

exportMethods("vsn2", "meanSdPlot", "predict", "logLik", "coef", "coefficients",
              "show", "exprs", "nrow", "ncol", "dim", "coerce")

