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.
BuildPalette            Builds a complete color palette for the
                        conditions given in argument
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.
GetDetailedNbPeptides   Computes the detailed number of peptides for
                        each protein
GetDetailedNbPeptidesUsed
                        Computes the detailed number of peptides used
                        for aggregating each protein
GetNbPeptidesUsed       Computes the number of peptides used for
                        aggregating each protein
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
GraphPepProt            Function to create a histogram that shows the
                        repartition of peptides w.r.t. the proteins
LH0                     xxxxxx
LH0.lm                  xxxxxx
LH1                     xxxxxx
LH1.lm                  xxxxxx
LOESS                   Normalisation LOESS
MeanCentering           Normalisation MeanCentering
NumericalFiltering      Removes lines in the dataset based on numerical
                        conditions.
NumericalgetIndicesOfLinesToRemove
                        Get the indices of the lines to delete, based
                        on a prefix string
QuantileCentering       Normalisation QuantileCentering
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
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'
buildGraph              Display a CC
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.
createMSnset            Creates an object of class 'MSnSet' from text
                        file
dapar_hc_ExportMenu     Customised contextual menu of highcharts plots
dapar_hc_chart          Customised resetZoomButton 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
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
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
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'.
limmaCompleteTest       Computes a hierarchical differential analysis
listSheets              This function returns the list of the sheets
                        names in a Excel file.
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
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_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
normalizeMethods.dapar
                        List normalization methods with tracking option
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
rbindMSnset             Similar to the function 'rbind' but applies on
                        two subsets of the same 'MSnSet' object.
reIntroduceMEC          Put back LAPALA into a 'MSnSet' object
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
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
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.CVDistD         Distribution of CV of entities
wrapper.CVDistD_HC      Distribution of CV of entities
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.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.KNN      KNN missing values imputation from a 'MSnSet'
                        object
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.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.
