NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(plot,safeQuantAnalysis)
S3method(print,safeQuantAnalysis)
export(.addPTMCoord)
export(.allpValueHist)
export(.correlationPlot)
export(.dotColorstrip)
export(.errorBar)
export(.exp2Exprs)
export(.filterSQA)
export(.getCalibMixEset)
export(.getCalibMixPairedEset)
export(.getConditionColors)
export(.getControlCondition)
export(.getFileType)
export(.getFirstEntry)
export(.getNbPlex)
export(.getProgenesisCsvExpressionColIndices)
export(.getProteaseRegExp)
export(.getSkipLineNb)
export(.getUniquePtmMotifs)
export(.idOverviewPlots)
export(.idPlots)
export(.intensityAdjustment)
export(.log2Exprs)
export(.outerLegend)
export(.plotCalibrationCurve)
export(.plotVolcano)
export(.qcPlots)
export(.setFilter)
export(COLORS)
export(addIdQvalues)
export(addScaffoldPTMFAnnotations)
export(barplotMSSignal)
export(createExpDesign)
export(createExpressionDataset)
export(createPairedExpDesign)
export(cvBoxplot)
export(cysteinFreqBarplot)
export(dotProduct)
export(expDesignTagToExpDesign)
export(expDesignTagToExpDesign_file_2)
export(export)
export(getAAProteinCoordinates)
export(getAccessionNumber)
export(getAllCV)
export(getAllDotProduct)
export(getAllEBayes)
export(getBaselineIntensity)
export(getCV)
export(getExpDesignProgenesisCsv)
export(getFTestPValue)
export(getGeneName)
export(getGlobalNormFactors)
export(getGoTermDF)
export(getIBAQEset)
export(getIdLevelQvals)
export(getImpuritiesMatrix)
export(getImputationMatrix)
export(getIntSumPerProtein)
export(getKinaseFreq)
export(getKinases)
export(getLOD)
export(getLoocvFoldError)
export(getMaxIndex)
export(getMeanCenteredRange)
export(getModifProteinCoordinates)
export(getMotifFreq)
export(getMotifX)
export(getNAFraction)
export(getNbDetectablePeptides)
export(getNbMisCleavages)
export(getNbPeptidesPerProtein)
export(getNbRolledUpFeatures)
export(getNbSpectraPerProtein)
export(getPeptides)
export(getRTNormFactors)
export(getRatios)
export(getScoreCutOff)
export(getSignalPerCondition)
export(getSwaths)
export(getTopX)
export(getUserOptions)
export(ggDilutionCurve)
export(ggVolcanoPlot)
export(globalNormalize)
export(hClustHeatMap)
export(hClustHeatMapOld)
export(isCon)
export(isDecoy)
export(isStrippedACs)
export(maPlotSQ)
export(missinValueBarplot)
export(option_list)
export(pairsAnnot)
export(parseDiaNNProteinGroupTxt)
export(parseMaxQuantProteinGroupTxt)
export(parseProgenesisFeatureCsv)
export(parseProgenesisPeptideMeasurementCsv)
export(parseProgenesisProteinCsv)
export(parseScaffoldPTMReport)
export(parseScaffoldRawFile)
export(parseSpectronantProteinGroupTxt)
export(perFeatureNormalization)
export(plotAbsEstCalibrationCurve)
export(plotAdjustedVsNonAdjustedRatio)
export(plotAllGGVolcanoes)
export(plotExpDesign)
export(plotIdScoreVsFDR)
export(plotLogo)
export(plotMSSignalDistributions)
export(plotNbIdentificationsVsRT)
export(plotNbValidDeFeaturesPerFDR)
export(plotPrecMassErrorDistrib)
export(plotPrecMassErrorVsScore)
export(plotQValueVsPValue)
export(plotROC)
export(plotRTNorm)
export(plotRTNormSummary)
export(plotScoreDistrib)
export(plotVolcano)
export(plotXYDensity)
export(purityCorrectTMT)
export(removeOutliers)
export(rollUp)
export(rollUpDT)
export(rtNormalize)
export(safeQuantAnalysis)
export(setNbPeptidesPerProtein)
export(setNbSpectraPerProtein)
export(sqImpute)
export(sqNormalize)
export(stripACs)
import(Biobase)
import(GO.db)
import(corrplot)
import(data.table)
import(epiR)
import(ggplot2)
import(ggrepel)
import(gplots)
import(impute)
import(limma)
import(magrittr)
import(optparse)
import(stringr)
importFrom(UniProt.ws,select)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(grDevices,densCols)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,boxplot)
importFrom(graphics,grid)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(pcaMethods,pca)
importFrom(seqinr,read.fasta)
importFrom(stats,IQR)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)