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A B C D E F G H I L M N P Q R S T U V W
| addOriginOfValue | Sets the OriginOfValues dataframe |
| aggregateIter | xxxx |
| aggregateIterParallel | xxxx |
| aggregateMean | Compute the intensity of proteins as the mean of the intensities of their peptides. |
| 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. |
| averageIntensities | Average protein/peptide abundances for each condition studied |
| 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 library 'highcharter' |
| BuildAdjacencyMatrix | Function matrix of appartenance group |
| BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by using the previous peptide dataset. |
| BuildColumnToProteinDataset_par | creates a column for the protein dataset after agregation by using the previous peptide dataset. |
| buildGraph | Display a CC |
| BuildPalette | Builds a complete color palette for the conditions given in argument |
| check.conditions | Check if the design is valid |
| check.design | Check if the design is valid |
| checkClusterability | Prepare the data for subsequent clustering |
| 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_t_tests | xxxxxx |
| corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'exprs()' table. |
| CountPep | Compute the number of peptides used to aggregate proteins |
| createMSnset | Creates an object of class 'MSnSet' from text file |
| CVDistD | Distribution of CV of entities |
| CVDistD_HC | Distribution of CV of entities |
| 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 | Builds a densityplot from a dataframe |
| densityPlotD_HC | Builds a densityplot from a dataframe |
| 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 |
| enrich_GO | Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance. |
| finalizeAggregation | Finalizes the aggregation process |
| findMECBlock | Finds the LAPALA into a 'MSnSet' object |
| formatLimmaResult | xxxx |
| formatPHResults | Extract logFC and raw pvalues from multiple post-hoc models summaries |
| fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic |
| get.pep.prot.cc | Build the list of connex composant of the adjacency matrix |
| 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 |
| getListNbValuesInLines | Returns the possible number of values in lines in the data |
| GetNbPeptidesUsed | Computes the number of peptides used for aggregating each protein |
| 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 |
| 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 |
| Get_AllComparisons | Returns list that contains a list of the statistical tests performed with DAPAR and recorded in an object of class 'MSnSet'. |
| 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 |
| hc_logFC_DensityPlot | Density plots of logFC values |
| hc_mvTypePlot2 | Distribution of Observed values with respect to intensity values |
| heatmap.DAPAR | This function is inspired from the function 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'. For more information, please refer to the help of the heatmap.2 function. |
| heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet' |
| histPValue_HC | Plots a histogram ov p-values |
| impute.detQuant | Deterministic imputation |
| impute.pa2 | Missing values imputation from a 'MSnSet' object |
| inner.aggregate.iter | xxxx |
| inner.aggregate.topn | xxxx |
| inner.mean | xxxx |
| inner.sum | xxxx |
| is.MV | Similar to the function 'is.na' but focused on the equality with the missing values in the dataset (type 'POV' and 'MEC') |
| is.OfType | Similar to the function 'is.na' but focused on the equality with the paramter 'type'. |
| 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 |
| 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 |
| MeanCentering | Normalisation MeanCentering |
| mvFilter | Filter lines in the matrix of intensities w.r.t. some criteria |
| mvFilterFromIndices | Filter lines in the matrix of intensities w.r.t. some criteria |
| mvFilterGetIndices | Filter lines in the matrix of intensities w.r.t. some criteria |
| mvHisto_HC | Histogram of missing values |
| mvImage | Heatmap of missing values |
| mvPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per condition |
| mvPerLinesHisto_HC | Bar plot of missing values per lines using highcharter |
| my_hc_chart | Customised resetZoomButton of highcharts plots |
| my_hc_ExportMenu | Customised contextual menu of highcharts plots |
| 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 |
| pepa.test | PEptide based Protein differential Abundance test |
| 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 |
| QuantileCentering | Normalisation QuantileCentering |
| 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. |
| 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' |
| setMEC | Sets the MEC tag in the OriginOfValues |
| 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 |
| test.design | Check if xxxxxx |
| translatedRandomBeta | Generator of simulated values |
| univ_AnnotDbPkg | Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF |
| violinPlotD | Builds a violinplot from a dataframe |
| visualizeClusters | Visualize the clusters according to pvalue thresholds |
| vsn | Normalisation vsn |
| wrapper.compareNormalizationD_HC | Builds a plot from a dataframe |
| wrapper.corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'exprs()' table |
| wrapper.CVDistD | Distribution of CV of entities |
| wrapper.CVDistD_HC | Distribution of CV of entities |
| wrapper.dapar.impute.mi | Missing values imputation using the LSimpute algorithm. |
| wrapper.hc_mvTypePlot2 | Distribution of observed values with respect to intensity values from a 'MSnSet' object |
| wrapper.heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the '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.mvHisto_HC | Histogram of missing values from a 'MSnSet' object |
| wrapper.mvImage | Heatmap of missing values from a 'MSnSet' object |
| wrapper.mvPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per conditions from an object 'MSnSet' |
| wrapper.mvPerLinesHisto_HC | Histogram of missing values per lines from an object using highcharter 'MSnSet' |
| 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 | Run a clustering pipeline of protein/peptide abundance profiles. |
| 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. |