
importFrom("methods", "show")
importClassesFrom(cellHTS2, cellHTS)
importMethodsFrom(cellHTS2, Data, lines, plate, well, pdim)
importFrom(RColorBrewer,brewer.pal)
importFrom(ICSNP, HotellingsT2)
importFrom(geneplotter, multidensity)
importFrom(grid, unit, unit.c, gpar, gTree, gList, vpPath, grid.draw, viewport, pushViewport, popViewport, downViewport, upViewport, vpTree, vpList, grid.layout, grid.raster, grid.rect, grid.text, grid.polyline, convertWidth, convertHeight, stringWidth, stringHeight, rectGrob, xaxisGrob, yaxisGrob, textGrob, linesGrob, pointsGrob)
importFrom(gplots, balloonplot)
importFrom(hwriter, closePage, hwrite, hwriteImage, openPage)
importFrom(lattice, levelplot, panel.axis, panel.levelplot)
importFrom(latticeExtra, dendrogramGrob)
importFrom(limma, eBayes, lmFit)
importFrom(splots, plotScreen)

importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
           "pdf", "png", "rainbow")
importFrom("graphics", "legend", "par", "points", "smoothScatter")
importFrom("methods", "getClassDef", "is", "new")
importFrom("stats", "C", "as.dendrogram", "cor", "df", "dist",
           "fisher.test", "hclust", "lm", "mad", "median", "medpolish",
           "order.dendrogram", "p.adjust", "prcomp", "predict", "pt",
           "quantile", "sd")
importFrom("utils", "read.table", "write.table")
importFrom("Biobase", "assayDataNew")
import(abind)
import(locfit)

## classes
exportClasses(RNAinteract)

# creating an RNAinteract object
export(createCellHTSFromFiles)
export(createRNAinteract)
export(createRNAinteractFromFiles)

# data access
export(getData)
export(getMain)
export(getMainNeg)

export(getReplicateData)
export(getIndDesignData)

export(getChannelNames)
export(getScreenNames)
export(getScale)

# subsetting and bind screen
export(sgisubset)
export(bindscreens)
export(summarizeScreens)

# main analysis and normalization
export(estimateMainEffect)
export(normalizeMainEffectQuery)
export(normalizeMainEffectTemplate)
export(normalizePlateEffect)
export(computePI)
export(computePValues)

#embedding
export(embedPCA)

# plotting
export(plotDoublePerturbation)
export(doublePerturbationGrob)
export(grid.doublePerturbation)
export(postDrawDetails.doublePerturbation)

export(plotHeatmap)
export(grid.sgiHeatmap)

# HTML report
export(startReport, endReport)
export(reportAnnotation)
export(reportDoublePerturbation)
export(reportGeneLists)
export(reportHeatmap)
export(reportMainEffects)
export(reportNetworks)
export(reportScreenData)
export(reportStatistics)

# Waiting for export

## export(getCellHTSObject)
## export(sgisubsetQueryDesign)
## export(plotIndDesignScatter)
## export(plotMainEffects)
## export(plotReplicateScatter)
## export(plotScatterErrorbars)
## export(plotScreenData)
## export(getTransformation)
## export(getInvTransformation)

## export(ordertree)
## export(swaptree)

## export(zPrime)

## export(grid.sgiColorkey)
## export(grid.sgiDendrogram)
