Tools for the Differential Analysis of Proteins Abundance with R
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Documentation for package ‘DAPAR’ version 1.41.0
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A B C D E F G H I L M N O P Q R S T U V W
-- A --
| aggregateIter | xxxx |
| aggregateIterParallel | xxxx |
| aggregateMean | Compute the intensity of proteins as the mean of the intensities of their peptides. |
| AggregateMetacell | Symbolic product of matrices |
| aggregateSum | Compute the intensity of proteins with the sum of the intensities of their peptides. |
| aggregateTopn | Compute the intensity of proteins as the sum of the intensities of their n best peptides. |
| applyAnovasOnProteins | iteratively applies OWAnova() on the features of an MSnSet object |
| averageIntensities | Average protein/peptide abundances for each condition studied |
-- B --
| barplotEnrichGO_HC | A barplot that shows the result of a GO enrichment, using the package 'highcharter' |
| barplotGroupGO_HC | A barplot which shows the result of a GO classification, using the package 'highcharter' |
| boxPlotD_HC | Builds a boxplot from a dataframe using the package 'highcharter' |
| BuildAdjacencyMatrix | Function matrix of appartenance group |
| BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by using the previous peptide dataset. |
| buildGraph | Display a CC |
| BuildMetaCell | Builds cells metadata |
-- C --
| check.conditions | Check if the design is valid |
| check.design | Check if the design is valid |
| checkClusterability | xxx |
| Check_Dataset_Validity | xxx |
| Check_NbValues_In_Columns | xxx |
| Children | Names of all chidren of a node |
| classic1wayAnova | Function to perform a One-way Anova statistical test on a MsnBase dataset |
| compareNormalizationD_HC | Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'highcharter' |
| compute.selection.table | Applies an FDR threshold on a table of adjusted p-values and summarizes the results |
| compute_t_tests | xxxxxx |
| corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table. |
| CountPep | Compute the number of peptides used to aggregate proteins |
| createMSnset | Creates an object of class 'MSnSet' from text file |
| createMSnset2 | Creates an object of class 'MSnSet' from text file |
| CVDistD_HC | Distribution of CV of entities |
-- D --
| dapar_hc_chart | Customised resetZoomButton of highcharts plots |
| dapar_hc_ExportMenu | Customised contextual menu of highcharts plots |
| deleteLinesFromIndices | Delete the lines in the matrix of intensities and the metadata table given their indice. |
| densityPlotD_HC | Builds a densityplot from a dataframe |
| diffAnaComputeAdjustedPValues | Computes the adjusted p-values |
| diffAnaComputeFDR | Computes the FDR corresponding to the p-values of the differential analysis using |
| diffAnaGetSignificant | Returns a MSnSet object with only proteins significant after differential analysis. |
| diffAnaSave | Returns a 'MSnSet' object with the results of the differential analysis performed with 'limma' package. |
| diffAnaVolcanoplot | Volcanoplot of the differential analysis |
| diffAnaVolcanoplot_rCharts | Volcanoplot of the differential analysis |
| display.CC.visNet | Display a CC |
-- E --
| enrich_GO | Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance. |
| ExtendPalette | Extends a base-palette of the package RColorBrewer to n colors. |
-- F --
| finalizeAggregation | Finalizes the aggregation process |
| findMECBlock | Finds the LAPALA into a 'MSnSet' object |
| formatHSDResults | xxx |
| formatLimmaResult | xxxx |
| formatPHResults | Extract logFC and raw pvalues from multiple post-hoc models summaries |
| formatPHTResults | xxx |
| fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic |
-- G --
| get.pep.prot.cc | Build the list of connex composant of the adjacency matrix |
| GetCC | Returns the contains of the slot processing of an object of class 'MSnSet' |
| GetColorsForConditions | Builds a complete color palette for the conditions given in argument |
| getDesignLevel | xxx |
| GetDetailedNbPeptides | Computes the detailed number of peptides for each protein |
| GetDetailedNbPeptidesUsed | Computes the detailed number of peptides used for aggregating each protein |
| getIndicesConditions | Gets the conditions indices. |
| getIndicesOfLinesToRemove | Get the indices of the lines to delete, based on a prefix string |
| GetIndices_BasedOnConditions | Search lines which respects request on one or more conditions. |
| GetIndices_MetacellFiltering | Delete the lines in the matrix of intensities and the metadata table given their indice. |
| GetIndices_WholeLine | Search lines which respects query on all their elements. |
| GetIndices_WholeMatrix | Search lines which respects request on one or more conditions. |
| GetKeyId | xxxx |
| getListNbValuesInLines | Returns the possible number of values in lines in the data |
| GetMatAdj | Returns the contains of the slot processing of an object of class 'MSnSet' |
| GetMetacell | xxxx |
| GetMetacellTags | List of metacell tags |
| GetNbPeptidesUsed | Computes the number of peptides used for aggregating each protein |
| GetNbTags | Number of each metacell tags |
| getNumberOf | Number of lines with prefix |
| getNumberOfEmptyLines | Returns the number of empty lines in the data |
| getPourcentageOfMV | Percentage of missing values |
| getProcessingInfo | Returns the contains of the slot processing of an object of class 'MSnSet' |
| getProteinsStats | Computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two. |
| getQuantile4Imp | Quantile imputation value definition |
| GetSoftAvailables | The set of softwares available |
| getTextForAggregation | Build the text information for the Aggregation process |
| getTextForAnaDiff | Build the text information for the Aggregation process |
| getTextForFiltering | Build the text information for the filtering process |
| getTextForGOAnalysis | Build the text information for the Aggregation process |
| getTextForHypothesisTest | Build the text information for the hypothesis test process |
| getTextForNewDataset | Build the text information for a new dataset |
| getTextForNormalization | Build the text information for the Normalization process |
| getTextForpeptideImputation | Build the text information for the peptide Imputation process |
| getTextForproteinImputation | Build the text information for the protein Imputation process |
| GetTypeofData | xxxx |
| GetUniqueTags | xxxx |
| Get_AllComparisons | Returns list that contains a list of the statistical tests performed with DAPAR and recorded in an object of class 'MSnSet'. |
| globalAdjPval | Computes the adjusted p-values on all the stacked contrasts using CP4P |
| GlobalQuantileAlignment | Normalisation GlobalQuantileAlignement |
| GOAnalysisSave | Returns an 'MSnSet' object with the results of the GO analysis performed with the functions 'enrichGO' and/or 'groupGO' of the 'clusterProfiler' package. |
| GraphPepProt | Function to create a histogram that shows the repartition of peptides w.r.t. the proteins |
| group_GO | Calculates the GO profile of a vector of genes/proteins at a given level of the Gene Ontology |
-- H --
| hc_logFC_DensityPlot | Density plots of logFC values |
| hc_mvTypePlot2 | Distribution of Observed values with respect to intensity values |
| heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet' |
| heatmapForMissingValues | xxx |
| histPValue_HC | Plots a histogram ov p-values |
-- I --
| impute.pa2 | Missing values imputation from a 'MSnSet' object |
| inner.aggregate.iter | xxxx |
| inner.aggregate.topn | xxxx |
| inner.mean | xxxx |
| inner.sum | xxxx |
| is.subset | xxx |
-- L --
| LH0 | xxxxxx |
| LH0.lm | xxxxxx |
| LH1 | xxxxxx |
| LH1.lm | xxxxxx |
| limmaCompleteTest | Computes a hierarchical differential analysis |
| listSheets | This function returns the list of the sheets names in a Excel file. |
| LOESS | Normalisation LOESS |
-- M --
| make.contrast | Builds the contrast matrix |
| make.design | Builds the design matrix |
| make.design.1 | Builds the design matrix for designs of level 1 |
| make.design.2 | Builds the design matrix for designs of level 2 |
| make.design.3 | Builds the design matrix for designs of level 3 |
| match.metacell | Similar to the function 'is.na' but focused on the equality with the paramter 'type'. |
| MeanCentering | Normalisation MeanCentering |
| metacell.def | Metadata vocabulary for entities |
| MetaCellFiltering | Filter lines in the matrix of intensities w.r.t. some criteria |
| MetacellFilteringScope | Lists the metacell scopes for filtering |
| metacellHisto_HC | Histogram of missing values |
| metacellPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per condition |
| metacellPerLinesHisto_HC | Bar plot of missing values per lines using highcharter |
| Metacell_DIA_NN | Sets the metacell dataframe for datasets which are from Dia-NN software |
| Metacell_generic | Sets the metacell dataframe for dataset without information about the origin of identification |
| Metacell_maxquant | Sets the metacell dataframe |
| Metacell_proline | Sets the metacell dataframe for datasets which are from Proline software |
| metacombine | Combine peptide metadata to build protein metadata |
| mvImage | Heatmap of missing values |
| my_hc_chart | Customised resetZoomButton of highcharts plots |
| my_hc_ExportMenu | Customised contextual menu of highcharts plots |
-- N --
| nonzero | Retrieve the indices of non-zero elements in sparse matrices |
| normalizeMethods.dapar | List normalization methods with tracking option |
| NumericalFiltering | Removes lines in the dataset based on numerical conditions. |
| NumericalgetIndicesOfLinesToRemove | Get the indices of the lines to delete, based on a prefix string |
-- O --
| OWAnova | Applies aov() on a vector of protein abundances using the design derived from the sample names (simple aov wrapper) |
-- P --
| Parent | Parent name of a node |
| pepa.test | PEptide based Protein differential Abundance test |
| pkgs.require | Loads packages |
| plotJitter | Jitter plot of CC |
| plotJitter_rCharts | Display a a jitter plot for CC |
| plotPCA_Eigen | Plots the eigen values of PCA |
| plotPCA_Eigen_hc | Plots the eigen values of PCA with the highcharts library |
| plotPCA_Ind | Plots individuals of PCA |
| plotPCA_Var | Plots variables of PCA |
| postHocTest | Post-hoc tests for classic 1-way ANOVA |
| proportionConRev_HC | Barplot of proportion of contaminants and reverse |
-- Q --
| QuantileCentering | Normalisation QuantileCentering |
-- R --
| rbindMSnset | Similar to the function 'rbind' but applies on two subsets of the same 'MSnSet' object. |
| readExcel | This function reads a sheet of an Excel file and put the data into a data.frame. |
| reIntroduceMEC | Put back LAPALA into a 'MSnSet' object |
| removeLines | Removes lines in the dataset based on a prefix string. |
-- S --
| samLRT | xxxxxx |
| saveParameters | Saves the parameters of a tool in the pipeline of Prostar |
| scatterplotEnrichGO_HC | A dotplot that shows the result of a GO enrichment, using the package 'highcharter' |
| search.metacell.tags | Search pattern in metacell vocabulary |
| separateAdjPval | Computes the adjusted p-values separately on contrast using CP4P |
| SetCC | Returns the connected components |
| SetMatAdj | Record the adjacency matrices in a slot of the dataset of class 'MSnSet' |
| Set_POV_MEC_tags | Sets the MEC tag in the metacell |
| splitAdjacencyMat | splits an adjacency matrix into specific and shared |
| StringBasedFiltering | Removes lines in the dataset based on a prefix strings (contaminants, reverse or both). |
| StringBasedFiltering2 | Removes lines in the dataset based on a prefix strings. |
| SumByColumns | Normalisation SumByColumns |
| SymFilteringOperators | xxx |
-- T --
| test.design | Check if xxxxxx |
| testAnovaModels | Applies a statistical test on each element of a list of linear models |
| thresholdpval4fdr | xxx |
| translatedRandomBeta | Generator of simulated values |
-- U --
| univ_AnnotDbPkg | Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF |
| UpdateMetacellAfterImputation | Update the cells metadata tags after imputation |
-- V --
| violinPlotD | Builds a violinplot from a dataframe |
| visualizeClusters | Visualize the clusters according to pvalue thresholds |
| vsn | Normalisation vsn |
-- W --
| wrapper.compareNormalizationD_HC | Builds a plot from a dataframe |
| wrapper.corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table |
| wrapper.CVDistD_HC | Distribution of CV of entities |
| wrapper.dapar.impute.mi | Missing values imputation using the LSimpute algorithm. |
| wrapper.heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet' |
| wrapper.impute.detQuant | Wrapper of the function 'impute.detQuant()' for objects of class 'MSnSet' |
| wrapper.impute.fixedValue | Missing values imputation from a 'MSnSet' object |
| wrapper.impute.KNN | KNN missing values imputation from a 'MSnSet' object |
| wrapper.impute.mle | Imputation of peptides having no values in a biological condition. |
| wrapper.impute.pa | Imputation of peptides having no values in a biological condition. |
| wrapper.impute.pa2 | Missing values imputation from a 'MSnSet' object |
| wrapper.impute.slsa | Imputation of peptides having no values in a biological condition. |
| wrapper.mvImage | Heatmap of missing values from a 'MSnSet' object |
| wrapper.normalizeD | Normalisation |
| wrapper.pca | Compute the PCA |
| wrapperCalibrationPlot | Performs a calibration plot on an 'MSnSet' object, calling the 'cp4p' package functions. |
| wrapperClassic1wayAnova | Wrapper for One-way Anova statistical test |
| wrapperRunClustering | clustering pipeline of protein/peptide abundance profiles. |
| write.excel | This function exports a data.frame to a Excel file. |
| writeMSnsetToCSV | Exports a MSnset dataset into a zip archive containing three zipped CSV files. |
| writeMSnsetToExcel | This function exports a 'MSnSet' object to a Excel file. |