importFrom(methods, is, new)
importClassesFrom(Biobase, AnnotatedDataFrame, eSet, ExpressionSet, Versioned, VersionedBiobase)
importMethodsFrom(Biobase, exprs, pData)
importFrom(Biobase, addVigs2WinMenu)
importFrom(graphics, abline, axis, box, legend, lines, mtext, par, plot, polygon, rug, text, title)
importFrom(stats, density, integrate, median, qhyper, quantile)
importFrom(twilight, twilight.permute.pair, twilight.permute.unpair, twilight.teststat)

export(check.test.args, compareLists, getOverlap, OrderedList, overlap,
       plot.listComparison, plot.listComparisonOverlap, plot.OrderedList,
       plot.shuffledRandomScores, prepareData, preparePermutations,
       print.listComparison, print.listComparisonOverlap, print.OrderedList,
       print.shuffledRandomScores, scoreOrderComparison,
       scoreOrderComparisonBoth, scoreRankings, shuffledRandomScores, test.fc,
       test.t, test.z)

S3method(plot, OrderedList)
S3method(plot, listComparison)
S3method(plot, shuffledRandomScores)
S3method(plot, listComparisonOverlap)
S3method(print, OrderedList)
S3method(print, listComparison)
S3method(print, listComparisonOverlap)
S3method(print, shuffledRandomScores)
