##--------------------------------------------------
## classes
##--------------------------------------------------
importClassesFrom(affy, AffyBatch)
importClassesFrom(Biobase, NChannelSet)
importClassesFrom(Biobase, ExpressionSet)
importClassesFrom(beadarray, beadLevelData, ExpressionSetIllumina)
importClassesFrom(limma, MAList, RGList)

##--------------------------------------------------
## methods
##--------------------------------------------------
importMethodsFrom(Biobase, assayData, channel, dims, exprs,
                  fData, featureData, pData, phenoData, rowMedians,
                  sampleNames, protocolData)

importMethodsFrom(affy, Mbox, mm, pm)
importMethodsFrom(genefilter, plot)
importMethodsFrom(vsn, meanSdPlot)

##--------------------------------------------------
## ordinary functions & objects
##--------------------------------------------------
importFrom(affy, AffyRNAdeg, plotAffyRNAdeg)

importFrom(affyPLM, fitPLM, RLE, NUSE)

importFrom(Biobase, copySubstitute)

#importFrom(Cairo, Cairo)
importFrom(svglite, svglite)

importFrom(genefilter, dist2)

importFrom(graphics, abline, legend, lines, par, segments, text)

importFrom(grDevices, boxplot.stats, colorRampPalette, pdf, png, rgb)

importFrom(grid, gpar, grid.layout, frameGrob, placeGrob, rectGrob, unit)

importFrom(Hmisc, hoeffd)

importFrom(hwriter, closePage, hwrite, hmakeTag, hwriteImage, openPage)

importFrom(lattice, barchart, bwplot, densityplot, draw.key,
           levelplot, ltext, make.groups, packet.number,
           panel.bwplot, panel.smoothScatter, panel.superpose, panel.barchart,
           strip.default, trellis.par.get, trellis.par.set, xyplot)

importFrom(latticeExtra, dendrogramGrob)

importFrom(methods, as, is, new, slot, validObject)

importFrom(RColorBrewer, brewer.pal, brewer.pal.info)

importFrom(setRNG, setRNG)

importFrom(stats, as.dendrogram, as.dist, density, ecdf, fft, hclust, ks.test,
           na.omit, order.dendrogram, prcomp, quantile)

#importFrom(SVGAnnotation, addECMAScripts, convertCSSStylesToSVG, 
#           getMatplotSeries, getPlotPoints, getViewBox)

importFrom(utils, read.table, sessionInfo)

importFrom(XML, getNodeSet, xmlAttrs, "xmlAttrs<-", xmlChildren, xmlParse, xmlRoot, saveXML)

importFrom(gridSVG, gridsvg, dev.off, grid.garnish)

##--------------------------------------------------
## export
##--------------------------------------------------
exportClasses("aqmReportModule", "outlierDetection")

export("arrayQualityMetrics")
export("prepdata", "prepaffy")

export("aqm.writereport")

export("aqm.boxplot", "aqm.maplot",  "aqm.density", "aqm.probesmap",
       "aqm.meansd",  "aqm.heatmap", "aqm.pca",
       "aqm.rle",     "aqm.nuse",    "aqm.rnadeg", ## "aqm.qcstats",
       "aqm.pmmm",    "aqm.spatial")

export("addXYfromGAL")
export("outliers", "boxplotOutliers")


