ribiosExpression/NAMESPACE at master · bedapub/ribiosExpression · GitHub

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# Generated by roxygen2: do not edit by hand

S3method(plot,DesignContrast)
S3method(removeAllZeroVar,DesignContrast)
S3method(removeAllZeroVar,matrix)
S3method(rowscale,ExpressionSet)
S3method(writeVarMetadata,default)
export(DesignContrast)
export(`annotation<-`)
export(`exprs<-`)
export(`fData<-`)
export(`featureNames<-`)
export(`pData<-`)
export(annotation)
export(assayData)
export(assertFullRank)
export(avgReplicates)
export(dataFrameTwoVecs)
export(design2group)
export(eSetToLongTable)
export(exprs)
export(fData)
export(featureData)
export(featureNames)
export(fixDesignMatrixColnames)
export(fixEmptyColumnName)
export(grp2gmt)
export(grpFiles2gmt)
export(keepMaxStatProbe)
export(limmaDgeTable)
export(limmaTopTable2dgeTable)
export(matrixToLongTable)
export(medianReplicates)
export(mergeEset)
export(pData)
export(parseContrastStr)
export(parseDesignContrast)
export(parseDesignContrastFile)
export(parseDesignContrastStr)
export(phenoData)
export(poolReplicates)
export(readAnnotationFile)
export(readEset)
export(readExprsMatrix)
export(readFKtable)
export(readFeatureAnnotationFile)
export(readGct)
export(readGctCls)
export(readSampleAnnotationFile)
export(removeAllZeroVar)
export(removeColRank)
export(sampleNames)
export(sniffFeatureType)
export(splitPCA)
export(summarizeProbesets)
export(summarizeSamples)
export(truncateDgeTable)
export(writeCls)
export(writeEset)
export(writeGctCls)
export(writeSampleGroups)
export(writeVarMetadata)
exportClasses(DesignContrast)
exportMethods("contrastAnnotation<-")
exportMethods("contrastMatrix<-")
exportMethods("designMatrix<-")
exportMethods(annotate)
exportMethods(contrastAnnotation)
exportMethods(contrastMatrix)
exportMethods(contrastNames)
exportMethods(contrastSampleIndices)
exportMethods(designMatrix)
exportMethods(designVariables)
exportMethods(dispGroups)
exportMethods(exprsToLong)
exportMethods(formatGmt)
exportMethods(groups)
exportMethods(nContrast)
exportMethods(reannotate)
exportMethods(show)
exportMethods(writeGct)
importClassesFrom(Biobase,ExpressionSet)
importClassesFrom(Biobase,eSet)
importClassesFrom(limma,MArrayLM)
importFrom(Biobase,`annotation<-`)
importFrom(Biobase,`exprs<-`)
importFrom(Biobase,`fData<-`)
importFrom(Biobase,`featureNames<-`)
importFrom(Biobase,`pData<-`)
importFrom(Biobase,annotation)
importFrom(Biobase,assayData)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,featureData)
importFrom(Biobase,featureNames)
importFrom(Biobase,pData)
importFrom(Biobase,phenoData)
importFrom(Biobase,sampleNames)
importFrom(Biobase,storageMode)
importFrom(Biobase,varLabels)
importFrom(Biobase,varMetadata)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,`%v%`)
importFrom(Matrix,rankMatrix)
importFrom(circlize,colorRamp2)
importFrom(limma,makeContrasts)
importFrom(limma,normalizeBetweenArrays)
importFrom(methods,as)
importFrom(methods,new)
importFrom(openxlsx,addStyle)
importFrom(openxlsx,addWorksheet)
importFrom(openxlsx,createStyle)
importFrom(openxlsx,createWorkbook)
importFrom(openxlsx,saveWorkbook)
importFrom(openxlsx,writeData)
importFrom(ribiosAnnotation,guessFeatureType)
importFrom(ribiosArg,parseFactor)
importFrom(ribiosArg,parseStrings)
importFrom(ribiosIO,readMatrix)
importFrom(ribiosIO,read_cls)
importFrom(ribiosIO,read_exprs_matrix)
importFrom(ribiosIO,read_gct_matrix)
importFrom(ribiosIO,writeMatrix)
importFrom(ribiosIO,write_gct)
importFrom(ribiosPlot,pcaScores)
importFrom(ribiosPlot,royalbluered)
importFrom(ribiosUtils,assertFile)
importFrom(ribiosUtils,dfFactor)
importFrom(ribiosUtils,haltifnot)
importFrom(ribiosUtils,headtail)
importFrom(ribiosUtils,matchColumnIndex)
importFrom(ribiosUtils,putColsFirst)
importFrom(ribiosUtils,removeInvarCol)
importFrom(ribiosUtils,rowscale)
importFrom(ribiosUtils,sortByCol)
importFrom(ribiosUtils,summarizeRows)
importFrom(ribiosUtils,ulen)
importFrom(stats,cor)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,prcomp)
importFrom(stats,qt)
importFrom(stats,reshape)
importFrom(stats,sd)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(methods,show)