BuildAdjacencyMatrix    Function matrix of appartenance group
BuildColumnToProteinDataset
                        creates a column for the protein dataset after
                        agregation by using the previous peptide
                        dataset.
CountPep                Compute the number of peptides used to
                        aggregate proteins
GraphPepProt            Function to create a histogram that shows the
                        repartition of peptides w.r.t. the proteins
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.
UPSpep25                UPSpep25 dataset
boxPlotD                Builds a boxplot from a dataframe
compareNormalizationD   Builds a plot from a dataframe
corrMatrixD             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
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
diffAnaWelch            Performs a differential analysis on a 'MSnSet'
                        object using the Welch t-test
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
getPaletteForReplicates
                        Palette for 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.
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'
limmaCompleteTest       Computes a hierarchical differential analysis
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
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
mvTypePlot              Distribution of missing values with respect to
                        intensity values
normalizeD              Normalisation
pepAgregate             Function agregate peptides to proteins
proportionConRev        Barplot of proportion of contaminants and
                        reverse
removeLines             Removes lines in the dataset based on a prefix
                        string.
test                    Test dataset
testWithoutNA           Test dataset
varianceDistD           Distribution of variance of proteins
violinPlotD             Builds a violinplot from a dataframe
wrapper.boxPlotD        Wrapper to the boxplotD function on an object
                        'MSnSet'
wrapper.compareNormalizationD
                        Builds a plot from a dataframe
wrapper.corrMatrixD     Displays a correlation matrix of the
                        quantitative data of the 'exprs()' table
wrapper.densityPlotD    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.mvHisto         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.mvTypePlot      Distribution of missing values with respect to
                        intensity values from a 'MSnSet' object
wrapper.normalizeD      Normalisation
wrapper.varianceDistD   Distribution of variance of proteins
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.
