Files in samWieczorek/DAPAR
Tools for the Differential Analysis of Proteins Abundance with R

DESCRIPTION
NAMESPACE
R/DescriptiveStats.R R/DiffAnalysis.R R/agregation.R R/bioAnalysis.R R/compute.t.tests.R R/inOutFiles.R R/limmaAnalysis.R R/logText.R R/missingValuesFilter.R R/missingValuesImputation_PeptideLevel.R R/missingValuesImputation_ProteinLevel.R R/missingValuesPlots.R R/normalize.R R/pepa.R R/utils.R R/volcanoPlot.R
inst/CITATION
inst/NEWS.Rd
man/BuildAdjacencyMatrix.Rd man/BuildColumnToProteinDataset.Rd man/BuildColumnToProteinDataset_par.Rd man/CVDistD.Rd man/CVDistD_HC.Rd man/CountPep.Rd man/GOAnalysisSave.Rd man/GetNbPeptidesUsed.Rd man/GraphPepProt.Rd man/LH0.Rd man/LH0.lm.Rd man/LH1.Rd man/LH1.lm.Rd man/StringBasedFiltering.Rd man/StringBasedFiltering2.Rd man/addOriginOfValue.Rd man/aggregateIter.Rd man/aggregateIterParallel.Rd man/aggregateMean.Rd man/aggregateSum.Rd man/aggregateTopn.Rd man/barplotEnrichGO_HC.Rd man/barplotGroupGO_HC.Rd man/boxPlotD.Rd man/boxPlotD_HC.Rd man/check.conditions.Rd man/check.design.Rd man/compareNormalizationD.Rd man/compareNormalizationD_HC.Rd man/compute.t.tests.Rd man/corrMatrixD.Rd man/corrMatrixD_HC.Rd man/createMSnset.Rd man/deleteLinesFromIndices.Rd man/densityPlotD.Rd man/densityPlotD_HC.Rd man/diffAnaComputeFDR.Rd man/diffAnaGetSignificant.Rd man/diffAnaSave.Rd man/diffAnaVolcanoplot.Rd man/diffAnaVolcanoplot_rCharts.Rd man/enrich_GO.Rd man/finalizeAggregation.Rd man/findMECBlock.Rd man/formatLimmaResult.Rd man/fudge2LRT.Rd man/getIndicesConditions.Rd man/getIndicesOfLinesToRemove.Rd man/getListNbValuesInLines.Rd man/getNumberOf.Rd man/getNumberOfEmptyLines.Rd man/getPourcentageOfMV.Rd man/getProcessingInfo.Rd man/getProteinsStats.Rd man/getQuantile4Imp.Rd man/getTextForAggregation.Rd man/getTextForAnaDiff.Rd man/getTextForFiltering.Rd man/getTextForGOAnalysis.Rd man/getTextForHypothesisTest.Rd man/getTextForNewDataset.Rd man/getTextForNormalization.Rd man/getTextForpeptideImputation.Rd man/getTextForproteinImputation.Rd man/group_GO.Rd man/hc_logFC_DensityPlot.Rd man/hc_mvTypePlot2.Rd man/heatmap.DAPAR.Rd man/heatmapD.Rd man/impute.detQuant.Rd man/impute.pa2.Rd man/inner.aggregate.iter.Rd man/inner.aggregate.topn.Rd man/inner.mean.Rd man/inner.sum.Rd man/is.MV.Rd man/is.OfType.Rd man/limmaCompleteTest.Rd man/listSheets.Rd man/make.contrast.Rd man/make.design.1.Rd man/make.design.2.Rd man/make.design.3.Rd man/make.design.Rd man/mvFilter.Rd man/mvFilterFromIndices.Rd man/mvFilterGetIndices.Rd man/mvHisto.Rd man/mvHisto_HC.Rd man/mvImage.Rd man/mvPerLinesHisto.Rd man/mvPerLinesHistoPerCondition.Rd man/mvPerLinesHistoPerCondition_HC.Rd man/mvPerLinesHisto_HC.Rd man/my_hc_ExportMenu.Rd man/my_hc_chart.Rd man/nonzero.Rd man/pepa.test.Rd man/plotPCA_Eigen.Rd man/plotPCA_Eigen_hc.Rd man/plotPCA_Ind.Rd man/plotPCA_Var.Rd man/proportionConRev_HC.Rd man/rbindMSnset.Rd man/reIntroduceMEC.Rd man/readExcel.Rd man/removeLines.Rd man/samLRT.Rd man/saveParameters.Rd man/scatterplotEnrichGO_HC.Rd man/setMEC.Rd man/test.design.Rd man/translatedRandomBeta.Rd man/univ_AnnotDbPkg.Rd man/violinPlotD.Rd man/wrapper.CVDistD.Rd man/wrapper.CVDistD_HC.Rd man/wrapper.compareNormalizationD.Rd man/wrapper.compareNormalizationD_HC.Rd man/wrapper.corrMatrixD.Rd man/wrapper.corrMatrixD_HC.Rd man/wrapper.dapar.impute.mi.Rd man/wrapper.hc_mvTypePlot2.Rd man/wrapper.heatmapD.Rd man/wrapper.impute.KNN.Rd man/wrapper.impute.detQuant.Rd man/wrapper.impute.fixedValue.Rd man/wrapper.impute.mle.Rd man/wrapper.impute.pa.Rd man/wrapper.impute.pa2.Rd man/wrapper.impute.slsa.Rd man/wrapper.mvHisto.Rd man/wrapper.mvHisto_HC.Rd man/wrapper.mvImage.Rd man/wrapper.mvPerLinesHisto.Rd man/wrapper.mvPerLinesHistoPerCondition.Rd man/wrapper.mvPerLinesHistoPerCondition_HC.Rd man/wrapper.mvPerLinesHisto_HC.Rd man/wrapper.normalizeD.Rd man/wrapper.pca.Rd man/wrapper.t_test_Complete.Rd man/wrapperCalibrationPlot.Rd man/writeMSnsetToCSV.Rd man/writeMSnsetToExcel.Rd tests/testthat.R tests/testthat/test_Volcanoplot.R tests/testthat/test_agregation.R tests/testthat/test_descriptiveStatistics.R tests/testthat/test_differentialAnalysis.R tests/testthat/test_limmaAnalysis.R tests/testthat/test_missingValuesImputation.R tests/testthat/test_missingValuesPlots.R tests/testthat/test_mvFilter.R tests/testthat/test_normalisation.R tests/testthat/test_utils.R
vignettes/Prostar.bib
vignettes/Prostar_UserManual.Rnw
vignettes/images/GO_tab1.png
vignettes/images/GO_tab2.png
vignettes/images/GO_tab3.png
vignettes/images/GO_tab4.png
vignettes/images/Rcode.png
vignettes/images/agregation1.png
vignettes/images/agregation2.png
vignettes/images/anaDiff1.png
vignettes/images/anaDiff2.png
vignettes/images/anaDiff3.png
vignettes/images/anaDiff4.png
vignettes/images/convert_convert.png
vignettes/images/convert_dataID.png
vignettes/images/convert_exp_featdata.png
vignettes/images/convert_sampledata.png
vignettes/images/convert_selectfile.png
vignettes/images/defaultProstar1.png
vignettes/images/demomode.png
vignettes/images/desc_CVDist.png
vignettes/images/desc_CVDist_ZoomIn.png
vignettes/images/desc_CVDist_ZoomOut.png
vignettes/images/desc_boxplot.png
vignettes/images/desc_corrmatrix.png
vignettes/images/desc_density.png
vignettes/images/desc_fdata.png
vignettes/images/desc_heatmap.png
vignettes/images/desc_missValues.png
vignettes/images/desc_pdata.png
vignettes/images/desc_quantiData.png
vignettes/images/desc_varDist.png
vignettes/images/desc_violinplot.png
vignettes/images/export.png
vignettes/images/exportReport.png
vignettes/images/filter1.png
vignettes/images/filter2.png
vignettes/images/filter3.png
vignettes/images/imputation.png
vignettes/images/logSession.png
vignettes/images/normalisation.png
vignettes/images/open_msnset.png
vignettes/intro.Rnw
samWieczorek/DAPAR documentation built on Oct. 18, 2018, 5:37 a.m.