API for prostarproteomics/DAPAR
Tools for the Differential Analysis of Proteins Abundance with R
| Global functions | |
|---|---|
| .onAttach | Source code |
| AggregateMetacell | Man page Source code |
| BuildAdjacencyMatrix | Man page Source code |
| BuildColumnToProteinDataset | Man page Source code |
| BuildMetaCell | Man page Source code |
| CVDistD_HC | Man page Source code |
| Check_Dataset_Validity | Man page Source code |
| Check_NbValues_In_Columns | Man page Source code |
| Children | Man page Source code |
| CountPep | Man page Source code |
| ExtendPalette | Man page Source code |
| GOAnalysisSave | Man page Source code |
| GetCC | Man page Source code |
| GetColorsForConditions | Man page Source code |
| GetDetailedNbPeptides | Man page Source code |
| GetDetailedNbPeptidesUsed | Man page Source code |
| GetIndices_BasedOnConditions | Man page Source code |
| GetIndices_MetacellFiltering | Man page Source code |
| GetIndices_WholeLine | Man page Source code |
| GetIndices_WholeMatrix | Man page Source code |
| GetKeyId | Man page Source code |
| GetMatAdj | Man page Source code |
| GetMetacell | Man page Source code |
| GetMetacellTags | Man page Source code |
| GetNbPeptidesUsed | Man page Source code |
| GetNbTags | Man page Source code |
| GetSoftAvailables | Man page Source code |
| GetTypeofData | Man page Source code |
| GetUniqueTags | Man page Source code |
| Get_AllComparisons | Man page Source code |
| GlobalQuantileAlignment | Man page Source code |
| GraphPepProt | Man page Source code |
| LH0 | Man page Source code |
| LH0.lm | Man page Source code |
| LH1 | Man page Source code |
| LH1.lm | Man page Source code |
| LOESS | Man page Source code |
| MeanCentering | Man page Source code |
| MetaCellFiltering | Man page Source code |
| MetacellFilteringScope | Man page Source code |
| Metacell_DIA_NN | Man page Source code |
| Metacell_generic | Man page Source code |
| Metacell_maxquant | Man page Source code |
| Metacell_proline | Man page Source code |
| NumericalFiltering | Man page Source code |
| NumericalgetIndicesOfLinesToRemove | Man page Source code |
| OWAnova | Man page Source code |
| Parent | Man page Source code |
| QuantileCentering | Man page Source code |
| SetCC | Man page Source code |
| SetMatAdj | Man page Source code |
| Set_POV_MEC_tags | Man page Source code |
| StringBasedFiltering | Man page Source code |
| StringBasedFiltering2 | Man page Source code |
| SumByColumns | Man page Source code |
| SymFilteringOperators | Man page Source code |
| UpdateMetacellAfterImputation | Man page Source code |
| aggregateIter | Man page Source code |
| aggregateIterParallel | Man page Source code |
| aggregateMean | Man page Source code |
| aggregateSum | Man page Source code |
| aggregateTopn | Man page Source code |
| applyAnovasOnProteins | Man page Source code |
| averageIntensities | Man page Source code |
| barplotEnrichGO_HC | Man page Source code |
| barplotGroupGO_HC | Man page Source code |
| boxPlotD_HC | Man page Source code |
| buildGraph | Man page Source code |
| check.conditions | Man page Source code |
| check.design | Man page Source code |
| checkClusterability | Man page Source code |
| classic1wayAnova | Man page Source code |
| compareNormalizationD_HC | Man page Source code |
| compute.selection.table | Man page Source code |
| compute_t_tests | Man page Source code |
| corrMatrixD_HC | Man page Source code |
| createMSnset | Man page Source code |
| createMSnset2 | Man page Source code |
| dapar_hc_ExportMenu | Man page Source code |
| dapar_hc_chart | Man page Source code |
| deleteLinesFromIndices | Man page Source code |
| densityPlotD_HC | Man page Source code |
| diffAnaComputeAdjustedPValues | Man page Source code |
| diffAnaComputeFDR | Man page Source code |
| diffAnaGetSignificant | Man page Source code |
| diffAnaSave | Man page Source code |
| diffAnaVolcanoplot | Man page Source code |
| diffAnaVolcanoplot_rCharts | Man page Source code |
| display.CC.visNet | Man page Source code |
| enrich_GO | Man page Source code |
| finalizeAggregation | Man page Source code |
| findMECBlock | Man page Source code |
| formatHSDResults | Man page Source code |
| formatLimmaResult | Man page Source code |
| formatPHResults | Man page Source code |
| formatPHTResults | Man page Source code |
| fudge2LRT | Man page Source code |
| get.pep.prot.cc | Man page Source code |
| getDesignLevel | Man page Source code |
| getIndicesConditions | Man page Source code |
| getIndicesOfLinesToRemove | Man page Source code |
| getListNbValuesInLines | Man page Source code |
| getNumberOf | Man page Source code |
| getNumberOfEmptyLines | Man page Source code |
| getPourcentageOfMV | Man page Source code |
| getProcessingInfo | Man page Source code |
| getProteinsStats | Man page Source code |
| getQuantile4Imp | Man page Source code |
| getTextForAggregation | Man page Source code |
| getTextForAnaDiff | Man page Source code |
| getTextForFiltering | Man page Source code |
| getTextForGOAnalysis | Man page Source code |
| getTextForHypothesisTest | Man page Source code |
| getTextForNewDataset | Man page Source code |
| getTextForNormalization | Man page Source code |
| getTextForpeptideImputation | Man page Source code |
| getTextForproteinImputation | Man page Source code |
| globalAdjPval | Man page Source code |
| group_GO | Man page Source code |
| hc_logFC_DensityPlot | Man page Source code |
| hc_mvTypePlot2 | Man page Source code |
| heatmapD | Man page Source code |
| heatmapForMissingValues | Man page Source code |
| histPValue_HC | Man page Source code |
| impute.pa2 | Man page Source code |
| inner.aggregate.iter | Man page Source code |
| inner.aggregate.topn | Man page Source code |
| inner.mean | Man page Source code |
| inner.sum | Man page Source code |
| is.subset | Man page Source code |
| limmaCompleteTest | Man page Source code |
| listSheets | Man page Source code |
| make.contrast | Man page Source code |
| make.design | Man page Source code |
| make.design.1 | Man page Source code |
| make.design.2 | Man page Source code |
| make.design.3 | Man page Source code |
| match.metacell | Man page Source code |
| metacell.def | Man page Source code |
| metacellHisto_HC | Man page Source code |
| metacellPerLinesHistoPerCondition_HC | Man page Source code |
| metacellPerLinesHisto_HC | Man page Source code |
| metacombine | Man page Source code |
| mvImage | Man page Source code |
| my_hc_ExportMenu | Man page Source code |
| my_hc_chart | Man page Source code |
| nonzero | Man page Source code |
| normalizeMethods.dapar | Man page Source code |
| pepa.test | Man page Source code |
| pkgs.require | Man page Source code |
| plotJitter | Man page Source code |
| plotJitter_rCharts | Man page Source code |
| plotPCA_Eigen | Man page Source code |
| plotPCA_Eigen_hc | Man page Source code |
| plotPCA_Ind | Man page Source code |
| plotPCA_Var | Man page Source code |
| postHocTest | Man page Source code |
| proportionConRev_HC | Man page Source code |
| rbindMSnset | Man page Source code |
| reIntroduceMEC | Man page Source code |
| readExcel | Man page Source code |
| removeLines | Man page Source code |
| samLRT | Man page Source code |
| saveParameters | Man page Source code |
| scatterplotEnrichGO_HC | Man page Source code |
| search.metacell.tags | Man page Source code |
| separateAdjPval | Man page Source code |
| splitAdjacencyMat | Man page Source code |
| test.design | Man page Source code |
| testAnovaModels | Man page Source code |
| thresholdpval4fdr | Man page Source code |
| translatedRandomBeta | Man page Source code |
| univ_AnnotDbPkg | Man page Source code |
| violinPlotD | Man page Source code |
| visualizeClusters | Man page Source code |
| vsn | Man page Source code |
| wrapper.CVDistD_HC | Man page Source code |
| wrapper.compareNormalizationD_HC | Man page Source code |
| wrapper.corrMatrixD_HC | Man page Source code |
| wrapper.dapar.impute.mi | Man page Source code |
| wrapper.heatmapD | Man page Source code |
| wrapper.impute.KNN | Man page Source code |
| wrapper.impute.detQuant | Man page Source code |
| wrapper.impute.fixedValue | Man page Source code |
| wrapper.impute.mle | Man page Source code |
| wrapper.impute.pa | Man page Source code |
| wrapper.impute.pa2 | Man page Source code |
| wrapper.impute.slsa | Man page Source code |
| wrapper.mvImage | Man page Source code |
| wrapper.normalizeD | Man page Source code |
| wrapper.pca | Man page Source code |
| wrapperCalibrationPlot | Man page Source code |
| wrapperClassic1wayAnova | Man page Source code |
| wrapperRunClustering | Man page Source code |
| write.excel | Man page Source code |
| writeMSnsetToCSV | Man page Source code |
| writeMSnsetToExcel | Man page Source code |
