##--------------------------------------------------

## classes

##--------------------------------------------------

importClassesFrom(affy, AffyBatch)

importClassesFrom(Biobase, NChannelSet)

importClassesFrom(Biobase, ExpressionSet)

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")