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