Tools for the Differential Analysis of Proteins Abundance with R
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Documentation for package ‘DaparToolshed’ version 0.99.36
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A B C D E F G H I K L M N O P Q R S T U V W
-- A --
| Add2History | Add row to history |
| addColors | Exports a 'QFeatures' object to a Excel file. |
| Add_Aggregated_rowData | Aggregate an assay's quantitative features |
| Add_Item_to_Dataset | Adds an instance of 'SummarizedExperiment' to a 'QFeatures' object |
| adjacency-matrix-filter | Filter a peptide assay on the basis of its adjacency matrix. |
| AdjMatFilters | Filter a peptide assay on the basis of its adjacency matrix. |
| aggQmetacell | Aggregate an assay's quantitative features |
| aggregateFeatures4Prostar | Aggregate an assay's quantitative features |
| aggregateFeatures4Prostar-method | Aggregate an assay's quantitative features |
| aggregateMethods | Aggregate an assay's quantitative features |
| aggregateRedistribution | Aggregate an assay's quantitative features with shared peptide redistribution |
| aggregateRedistribution-method | Aggregate an assay's quantitative features with shared peptide redistribution |
| allPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| analysis | List of metacell tags |
| analysis-method | List of metacell tags |
| analysis<- | List of metacell tags |
| applyAnovasOnProteins | iteratively applies OWAnova() on the features of an MSnSet object |
-- B --
| BuildAdjacencyMatrix | Function matrix of appartenance group |
| BuildColumnToProteinDataset | Aggregate an assay's quantitative features |
| buildGraph | Display a CC |
| BuildMetacell | Metacell function |
-- C --
| checkConditions | Check if the design is valid |
| checkDesign | Check if the design is valid |
| Children | Names of all children of a node |
| classic1wayAnova | Function to perform a One-way Anova statistical test on a MsnBase dataset |
| CleanRowData | Clean row data |
| compareNormalizationD_HC | Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'plotly' |
| compute_t_tests | Compute a t-test |
| ConnectedComp | List of metacell tags |
| ConnectedComp-method | List of metacell tags |
| ConnectedComp<- | List of metacell tags |
| ConvertListToHtml | Convert a list to unnumbered HTML list |
| CountPep | Aggregate an assay's quantitative features |
| createQFeatures | Creates an object of class 'QFeatures' from text file. |
| custom_metacell_colors | Quantitative metadata vocabulary for entities |
-- D --
| DaparToolsehd, | Filter features of one SE based on their rowData |
| DaparToolshed-aggregate | Aggregate an assay's quantitative features |
| DaparToolshed-aggregateRedistribution | Aggregate an assay's quantitative features with shared peptide redistribution |
| design_qf | List of metacell tags |
| design_qf-method | List of metacell tags |
| design_qf<- | List of metacell tags |
| diffAnaComputeAdjustedPValues | Computes the adjusted p-values |
| diffAnaComputeFDR | Computes the FDR corresponding to the p-values of the differential analysis |
| diffAnaVolcanoplot_rCharts | Volcanoplot of the differential analysis |
| DifferentialAnalysis | List of metacell tags |
| DifferentialAnalysis-method | List of metacell tags |
| DifferentialAnalysis<- | List of metacell tags |
| displayCCvisNet | Display a CC |
-- E --
| ExtendPalette | Extends a base-palette of the package RColorBrewer to n colors. |
| ExtractUniquePeptides | Aggregate an assay's quantitative features |
-- F --
| filename | List of metacell tags |
| filename-method | List of metacell tags |
| filename<- | List of metacell tags |
| filterFeaturesOneSE | Filter features of one SE based on their rowData |
| filterFeaturesOneSE, | Filter features of one SE based on their rowData |
| filterFeaturesOneSE-method | Filter features of one SE based on their rowData |
| findMECBlock | Finds the LAPALA |
| formatHSDResults | Extracts the FC and the FWER ajusted p-values and format them in a data.frame |
| formatLimmaResult | Format Limma results |
| formatPHResults | Extract logFC and raw pvalues from multiple post-hoc models summaries |
| formatPHTResults | Extracts the FC and the raw p-values and format them in a data.frame |
| fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic |
| FunctionFilter | Filter features of one SE based on their rowData |
| FunctionFilter, | Filter features of one SE based on their rowData |
| FunctionFilter-class | Filter features of one SE based on their rowData |
-- G --
| GetColorsForConditions | Builds a complete color palette for the conditions given in argument |
| getDesignLevel | Get design level |
| GetDetailedNbPeptides | Aggregate an assay's quantitative features |
| GetDetailedNbPeptidesUsed | Aggregate an assay's quantitative features |
| GetHistory | Wrapper for the 'paramshistory' function. |
| GetIndices_BasedOnConditions | Search lines which respects request on one or more conditions. |
| GetIndices_FunFiltering | Delete the lines in the matrix of intensities and the metadata table given their indices. |
| GetIndices_WholeLine | Search lines which respects query on all their elements. |
| GetIndices_WholeMatrix | Search lines which respects request on one or more conditions. |
| getListNbValuesInLines | Returns the possible number of values in lines in the data |
| GetMetacellTags | List of metacell tags |
| GetMetacellTags-method | List of metacell tags |
| GetMetadataSlot | List of metacell tags |
| GetNbPeptidesUsed | Aggregate an assay's quantitative features |
| GetNbTags | Number of each metacell tags |
| getNumberOfEmptyLines | Returns the number of empty lines in the data |
| getPepProtCC | Build the list of connex composant of the adjacency matrix |
| getProteinsStats | Aggregate an assay's quantitative features |
| getQuantile4Imp | Finds the LAPALA |
| GetRowdataSlot | List of metacell tags |
| GetSoftAvailables | The set of available softwares to convert from |
| GetUniqueTags | List of metacell tags |
| GetUniqueTags-method | List of metacell tags |
| globalAdjPval | Computes the adjusted p-values on all the stacked contrasts using CP4P |
| GlobalQuantileAlignment | Normalisation |
| GraphPepProt | Aggregate an assay's quantitative features |
-- H --
| hc_logFC_DensityPlot | Density plots of logFC values |
| hc_mvTypePlot2 | Bar plot of missing values per lines using plotly |
| heatmapForMissingValues | Display a heatmap for data with missing values |
| histPValue_HC | Plots a histogram of p-values |
| HypothesisTest | List of metacell tags |
| HypothesisTest-method | List of metacell tags |
| HypothesisTest<- | List of metacell tags |
-- I --
| idcol | List of metacell tags |
| idcol-method | List of metacell tags |
| idcol<- | List of metacell tags |
| imputePA2 | Missing values imputation from a 'MSnSet' object |
| InitializeHistory | Initialize the history |
| innerAggregateIter | Aggregate an assay's quantitative features |
| innerMean | Aggregate an assay's quantitative features |
| innerMedian | Aggregate an assay's quantitative features |
| innerMedianpolish | Aggregate an assay's quantitative features |
| innerRobustsummary | Aggregate an assay's quantitative features |
| innerSum | Aggregate an assay's quantitative features |
| isDifferential | Identification of differentially abundant peptide/protein |
| isOfType | Similar to the function 'is.na()' but focused on the equality with the paramter 'type'. |
| isSubset | Check is a given set is a subset of another one. |
-- K --
| Keep_Items_from_Dataset | Removes assay from a 'QFeatures' object |
-- L --
| last_assay | Utility funcitons to dela with QFeatures objects. |
| LH0 | Compute the likelihood of the null hypothesis for the global model |
| LH0_lm | Compute the likelihoods of the null hypothesis for the "local" component-wise model |
| LH1 | Compute the likelihood of the alternative hypothesis for the global model |
| LH1_lm | Compute the likelihoods of the alternative hypothesis for the "local" component-wise model |
| limmaCompleteTest | Computes a hierarchical differential analysis |
| listSheets | This function exports a data.frame to a Excel file. |
| LOESS | Normalisation |
-- M --
| mainAssay | List of metacell tags |
| makeContrast | Builds the contrast matrix |
| makeDesign | Builds the design matrix |
| makeDesign1 | Builds the design matrix for designs of level 1 |
| makeDesign2 | Builds the design matrix for designs of level 2 |
| makeDesign3 | Builds the design matrix for designs of level 3 |
| matchMetacell | Similar to the function 'is.na()' but focused on the equality with the paramter 'type'. |
| MeanCentering | Normalisation |
| metacell-plots | Bar plot of missing values per lines using plotly |
| metacellDef | Quantitative metadata vocabulary for entities |
| MetacellFilteringScope | Lists the metacell scopes for filtering |
| metacellHisto_HC | Bar plot of missing values per lines using plotly |
| metacellPerLinesHistoPerCondition_HC | Bar plot of missing values per lines using plotly |
| metacellPerLinesHisto_HC | Bar plot of missing values per lines using plotly |
| metacell_agg | Aggregate an assay's quantitative features |
| Metacell_DIA_NN | Sets the metacell dataframe for datasets which are from Dia-NN software |
| Metacell_generic | Quantitative metadata vocabulary for entities |
| Metacell_maxquant | Sets the metacell dataframe |
| Metacell_proline | Sets the metacell dataframe for datasets which are from Proline software |
| metacombine | Quantitative metadata vocabulary for entities |
| mvImage | Bar plot of missing values per lines using plotly |
| mv_imputation_protein | Finds the LAPALA |
-- N --
| NAIsZero | Set NA values to 0 |
| names_metacell | List of metacell tags |
| names_metacell-method | List of metacell tags |
| names_metacell<- | List of metacell tags |
| nEmptyLines | Number of empty lines in the data |
| nonzero | Retrieve the indices of non-zero elements in sparse matrices |
| normalization_methods | Normalisation |
| normalizeFunction | Normalisation for QFeatures |
| normalizeMethods | Normalisation |
| n_assays_in_qf | Utility funcitons to dela with QFeatures objects. |
-- O --
| output_2_Excel | This function exports a data.frame to a Excel file. |
| OWAnova | Applies aov() on a vector of protein abundances using the design derived from the sample names (simple aov wrapper) |
-- P --
| paramshistory | List of metacell tags |
| paramshistory-method | List of metacell tags |
| paramshistory<- | List of metacell tags |
| Parent | Parent name of a node |
| parentProtId | List of metacell tags |
| parentProtId-method | List of metacell tags |
| parentProtId<- | List of metacell tags |
| pepaTest | PEptide based Protein differential Abundance test |
| Pipelines | List of available pipelines in the package |
| pkgsRequire | Loads packages |
| plotCompareAssays | Compare two assays |
| plotJitter | Jitter plot of CC |
| plotJitter_rCharts | Display a a jitter plot for CC |
| postHocTest | Post-hoc tests for classic 1-way ANOVA |
| pushpvalue | Push p-values based on metacell tags |
-- Q --
| QFeatures-accessors | List of metacell tags |
| QFeatures-excel | Exports a 'QFeatures' object to a Excel file. |
| QFeatures-filtering-oneSE | Filter features of one SE based on their rowData |
| QFeatures-utils | Utility funcitons to dela with QFeatures objects. |
| QFeaturesFromSE | Utility funcitons to dela with QFeatures objects. |
| qMetacell | List of metacell tags |
| qMetacell-filter | Search lines which respects request on one or more conditions. |
| qMetacell-method | List of metacell tags |
| qMetacell<- | List of metacell tags |
| qMetacellFilteringScope | Search lines which respects request on one or more conditions. |
| qMetacellOnConditions | Search lines which respects request on one or more conditions. |
| qMetacellWholeLine | Search lines which respects request on one or more conditions. |
| qMetacellWholeMatrix | Search lines which respects request on one or more conditions. |
| QuantileCentering | Normalisation |
| q_metacell | Quantitative metadata vocabulary for entities |
-- R --
| readExcel | This function exports a data.frame to a Excel file. |
| reIntroduceMEC | Finds the LAPALA |
| ReplaceSpecialChars | Standardize names |
| RunAggregation | Aggregate an assay's quantitative features |
-- S --
| samLRT | Computes a regularized version of the likelihood ratio statistic |
| searchMetacellTags | Quantitative metadata vocabulary for entities |
| select_topn | Aggregate an assay's quantitative features |
| separateAdjPval | Computes the adjusted p-values separately on contrast using CP4P |
| SetHistory | Standardize names |
| Set_POV_MEC_tags | Quantitative metadata vocabulary for entities |
| Set_POV_MEC_tags2 | Quantitative metadata vocabulary for entities |
| sharedPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| specPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| splitAdjacencyMat | splits an adjacency matrix into specific and shared |
| subAdjMat_sharedPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| subAdjMat_specificPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| subAdjMat_topnPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| subR25pept | subR25pept dataset |
| subR25prot | subR25prot dataset |
| SumByColumns | Normalisation |
| SymFilteringOperators | Search lines which respects request on one or more conditions. |
-- T --
| testAnovaModels | Applies a statistical test on each element of a list of linear models |
| testDesign | Check the validity of the design |
| thresholdpval4fdr | Applies p-value adjustment using cp4p on p-values below a given threshold |
| topnFunctions | Filter a peptide assay on the basis of its adjacency matrix. |
| topnPeptides | Filter a peptide assay on the basis of its adjacency matrix. |
| translatedRandomBeta | Generator of simulated values |
| typeDataset | List of metacell tags |
| typeDataset-method | List of metacell tags |
| typeDataset<- | List of metacell tags |
-- U --
| UpdateMetacellAfterImputation | Quantitative metadata vocabulary for entities |
| UpdateMetacellAfterImputation-method | Quantitative metadata vocabulary for entities |
-- V --
| VariableFilter | Filter features of one SE based on their rowData |
| version | List of metacell tags |
| version-method | List of metacell tags |
| version<- | List of metacell tags |
| vsn | Normalisation |
-- W --
| wrapperCalibrationPlot | Performs a calibration plot on an 'SummarizedExperiment' object, calling the 'cp4p' package functions. |
| wrapperClassic1wayAnova | Wrapper for One-way Anova statistical test |
| wrapperDaparImputeMI | Missing values imputation using the LSimpute algorithm. |
| wrapperImputeDetQuant | Finds the LAPALA |
| wrapperImputeFixedValue | Finds the LAPALA |
| wrapperImputeKNN | Finds the LAPALA |
| wrapperImputeMLE | Imputation of peptides having no values in a biological condition. |
| wrapperImputePA | Finds the LAPALA |
| wrapperImputePA2 | Missing values imputation from a 'SummarizedExperiment' object |
| wrapperImputeSLSA | Finds the LAPALA |
| wrapperMVImage | Bar plot of missing values per lines using plotly |
| wrapperPirat | Missing values imputation using Pirat |
| write2excel | Exports a 'QFeatures' object to a Excel file. |
| write2excel-method | Exports a 'QFeatures' object to a Excel file. |
| write2excelSE | Exports a 'QFeatures' object to a Excel file. |
| writeExcel | This function exports a data.frame to a Excel file. |
| WriteHistory | This function exports a data.frame to a Excel file. |
| write_Assay_To_Excel | This function exports a data.frame to a Excel file. |
| Write_RowData | This function exports a data.frame to a Excel file. |
| Write_SamplesData_to_Excel | This function exports a data.frame to a Excel file. |