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.
CVDistD                 Distribution of CV of entities
CVDistD_HC              Distribution of CV of entities
CountPep                Compute the number of peptides used to
                        aggregate proteins
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
LH0                     xxxxxx
LH1                     xxxxxx
MeanPeptides            Compute the intensity of proteins as the mean
                        of the intensities of their peptides.
SumPeptides             Compute the intensity of proteins with the sum
                        of the intensities of their peptides.
TopnPeptides            Compute the intensity of proteins as the sum of
                        the intensities of their n best peptides.
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                Builds a boxplot from a dataframe
boxPlotD_HC             Builds a boxplot from a dataframe using the
                        library 'highcharter'
compareNormalizationD   Builds a plot from a dataframe
compareNormalizationD_HC
                        Builds a plot from a dataframe. Same as
                        compareNormalizationD but uses the library
                        'highcharter'
corrMatrixD             Displays a correlation matrix of the
                        quantitative data of the 'exprs()' table.
corrMatrixD_HC          Displays a correlation matrix of the
                        quantitative data of the 'exprs()' table.
createMSnset            Creates an object of class 'MSnSet' from text
                        file
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
diffAna                 This function performs a differential analysis
                        on an MSnSet object (adapted from 'limma')
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.
diffAnaLimma            Performs differential analysis on an MSnSet
                        object, calling the 'limma' package functions
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
diffAnaWelch            Performs a differential analysis on a 'MSnSet'
                        object using the Welch t-test
enrich_GO               Calculates GO enrichment classes for a given
                        list of proteins/genes ID. It results an
                        enrichResult instance.
fudge2LRT               Heuristic to choose the value of the
                        hyperparameter (fudge factor) used to
                        regularize the variance estimator in the
                        likelihood ratio statistic
getIndicesConditions    Gets the conditions indices.
getIndicesOfLinesToRemove
                        Get the indices of the lines to delete, based
                        on a prefix string
getNumberOf             Number of lines with prefix
getNumberOfEmptyLines   Returns the number of empty lines in the data
getPaletteForLabels     Palette for plots in 'DAPAR'
getPaletteForLabels_HC
                        Palette for highcharter plots used in 'DAPAR'
getPaletteForReplicates
                        Palette for plot the replicates in 'DAPAR'
getPaletteForReplicates_HC
                        Palette for highcharter plot the replicates in
                        DAPAR
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
group_GO                Calculates the GO profile of a vector of
                        genes/proteins at a given level of the Gene
                        Ontology
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'
impute.detQuant         Deterministic imputation
impute.pa2              Missing values imputation from a 'MSnSet'
                        object
limmaCompleteTest       Computes a hierarchical differential analysis
listSheets              This function returns the list of the sheets
                        names in a Excel file.
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                 Histogram of missing values
mvHisto_HC              Histogram of missing values
mvImage                 Heatmap of missing values
mvImputation            Missing values imputation from a matrix
mvPerLinesHisto         Bar plot of missing values per lines
mvPerLinesHistoPerCondition
                        Bar plot of missing values per lines and per
                        condition
mvPerLinesHistoPerCondition_HC
                        Bar plot of missing values per lines and per
                        condition
mvPerLinesHisto_HC      Bar plot of missing values per lines using
                        highcharter
mvTypePlot              Distribution of missing values with respect to
                        intensity values
my_hc_ExportMenu        Customised contextual menu of highcharts plots
my_hc_chart             Customised resetZoomButton of highcharts plots
nonzero                 Retrieve the indices of non-zero elements in
                        sparse matrices
normalizeD              Normalisation
normalizeD2             Normalisation
pepAgregate             Function agregate peptides to proteins
pepa.test               PEptide based Protein differential Abundance
                        test
proportionConRev_HC     Barplot of proportion of contaminants and
                        reverse
readExcel               This function reads a sheet of an Excel file
                        and put the data into a data.frame.
removeLines             Removes lines in the dataset based on a prefix
                        string.
samLRT                  xxxxxx
scatterplotEnrichGO_HC
                        A dotplot that shows the result of a GO
                        enrichment, using the package 'highcharter'
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
wrapper.CVDistD         Distribution of CV of entities
wrapper.CVDistD_HC      Distribution of CV of entities
wrapper.boxPlotD        Wrapper to the boxplotD function on an object
                        'MSnSet'
wrapper.boxPlotD_HC     Wrapper to the boxplotD_HC function on an
                        object 'MSnSet'
wrapper.compareNormalizationD
                        Builds a plot from a dataframe
wrapper.compareNormalizationD_HC
                        Builds a plot from a dataframe
wrapper.corrMatrixD     Displays a correlation matrix of the
                        quantitative data of the 'exprs()' table
wrapper.corrMatrixD_HC
                        Displays a correlation matrix of the
                        quantitative data of the 'exprs()' table
wrapper.dapar.impute.mi
                        Missing values imputation using the LSimpute
                        algorithm.
wrapper.densityPlotD    Builds a densityplot from an object of class
                        'MSnSet'
wrapper.densityPlotD_HC
                        Builds a densityplot from an object of class
                        'MSnSet'
wrapper.diffAnaLimma    Performs differential analysis on an MSnSet
                        object, calling the 'limma' package functions
wrapper.diffAnaWelch    Performs a differential analysis on a 'MSnSet'
                        object using the Welch t-test
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.pa       Imputation of peptides having no values in a
                        biological condition.
wrapper.impute.pa2      Missing values imputation from a 'MSnSet'
                        object
wrapper.mvHisto         Histogram of missing values from a 'MSnSet'
                        object
wrapper.mvHisto_HC      Histogram of missing values from a 'MSnSet'
                        object
wrapper.mvImage         Heatmap of missing values from a 'MSnSet'
                        object
wrapper.mvImputation    Missing values imputation from a 'MSnSet'
                        object
wrapper.mvPerLinesHisto
                        Histogram of missing values per lines from an
                        object 'MSnSet'
wrapper.mvPerLinesHistoPerCondition
                        Bar plot of missing values per lines and per
                        conditions from an object 'MSnSet'
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.mvTypePlot      Distribution of missing values with respect to
                        intensity values from a 'MSnSet' object
wrapper.normalizeD      Normalization
wrapper.normalizeD2     Normalisation
wrapper.violinPlotD     Wrapper to the violinPlotD function on an
                        object 'MSnSet'
wrapperCalibrationPlot
                        Performs a calibration plot on an 'MSnSet'
                        object, calling the 'cp4p' package functions.
writeMSnsetToExcel      This function exports a 'MSnSet' object to a
                        Excel file.
