Add2History             Add row to history
Add_Item_to_Dataset     Adds an instance of 'SummarizedExperiment' to a
                        'QFeatures' object
BuildAdjacencyMatrix    Function matrix of appartenance group
BuildMetacell           Metacell function
Children                Names of all children of a node
CleanRowData            Clean row data
ConvertListToHtml       Convert a list to unnumbered HTML list
DaparToolshed-aggregate
                        Aggregate an assay's quantitative features
DaparToolshed-aggregateRedistribution
                        Aggregate an assay's quantitative features with
                        shared peptide redistribution
ExtendPalette           Extends a base-palette of the package
                        RColorBrewer to n colors.
GetColorsForConditions
                        Builds a complete color palette for the
                        conditions given in argument
GetHistory              Wrapper for the 'paramshistory' function.
GetIndices_BasedOnConditions
                        Search lines which respects request on one or
                        more conditions.
GetIndices_FunFiltering
                        Delete the lines in the matrix of intensities
                        and the metadata table given their indices.
GetIndices_WholeLine    Search lines which respects query on all their
                        elements.
GetIndices_WholeMatrix
                        Search lines which respects request on one or
                        more conditions.
GetNbTags               Number of each metacell tags
GetSoftAvailables       The set of available softwares to convert from
InitializeHistory       Initialize the history
Keep_Items_from_Dataset
                        Removes assay from a 'QFeatures' object
LH0                     Compute the likelihood of the null hypothesis
                        for the global model
LH0_lm                  Compute the likelihoods of the null hypothesis
                        for the "local" component-wise model
LH1                     Compute the likelihood of the alternative
                        hypothesis for the global model
LH1_lm                  Compute the likelihoods of the alternative
                        hypothesis for the "local" component-wise model
MetacellFilteringScope
                        Lists the metacell scopes for filtering
Metacell_DIA_NN         Sets the metacell dataframe for datasets which
                        are from Dia-NN software
Metacell_maxquant       Sets the metacell dataframe
Metacell_proline        Sets the metacell dataframe for datasets which
                        are from Proline software
NAIsZero                Set NA values to 0
OWAnova                 Applies aov() on a vector of protein abundances
                        using the design derived from the sample names
                        (simple aov wrapper)
Parent                  Parent name of a node
Pipelines               List of available pipelines in the package
QFeatures-excel         Exports a 'QFeatures' object to a Excel file.
QFeatures-filtering-oneSE
                        Filter features of one SE based on their
                        rowData
QFeatures-utils         Utility funcitons to dela with QFeatures
                        objects.
ReplaceSpecialChars     Standardize names
SetHistory              Standardize names
SymFilteringOperators   Search lines which respects request on one or
                        more conditions.
adjacency-matrix-filter
                        Filter a peptide assay on the basis of its
                        adjacency matrix.
applyAnovasOnProteins   iteratively applies OWAnova() on the features
                        of an MSnSet object
buildGraph              Display a CC
checkConditions         Check if the design is valid
checkDesign             Check if the design is valid
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
                        'plotly'
compute_t_tests         Compute a t-test
createQFeatures         Creates an object of class 'QFeatures' from
                        text file.
diffAnaComputeAdjustedPValues
                        Computes the adjusted p-values
diffAnaComputeFDR       Computes the FDR corresponding to the p-values
                        of the differential analysis
diffAnaVolcanoplot_rCharts
                        Volcanoplot of the differential analysis
displayCCvisNet         Display a CC
formatHSDResults        Extracts the FC and the FWER ajusted p-values
                        and format them in a data.frame
formatLimmaResult       Format Limma results
formatPHResults         Extract logFC and raw pvalues from multiple
                        post-hoc models summaries
formatPHTResults        Extracts the FC and the raw p-values and format
                        them in a data.frame
fudge2LRT               Heuristic to choose the value of the
                        hyperparameter (fudge factor) used to
                        regularize the variance estimator in the
                        likelihood ratio statistic
getDesignLevel          Get design level
getListNbValuesInLines
                        Returns the possible number of values in lines
                        in the data
getNumberOfEmptyLines   Returns the number of empty lines in the data
getPepProtCC            Build the list of connex composant of the
                        adjacency matrix
globalAdjPval           Computes the adjusted p-values on all the
                        stacked contrasts using CP4P
hc_logFC_DensityPlot    Density plots of logFC values
heatmapForMissingValues
                        Display a heatmap for data with missing values
histPValue_HC           Plots a histogram of p-values
imputePA2               Missing values imputation from a 'MSnSet'
                        object
isDifferential          Identification of differentially abundant
                        peptide/protein
isOfType                Similar to the function 'is.na()' but focused
                        on the equality with the paramter 'type'.
isSubset                Check is a given set is a subset of another
                        one.
limmaCompleteTest       Computes a hierarchical differential analysis
makeContrast            Builds the contrast matrix
makeDesign              Builds the design matrix
makeDesign1             Builds the design matrix for designs of level 1
makeDesign2             Builds the design matrix for designs of level 2
makeDesign3             Builds the design matrix for designs of level 3
matchMetacell           Similar to the function 'is.na()' but focused
                        on the equality with the paramter 'type'.
metacell-plots          Bar plot of missing values per lines using
                        plotly
mv_imputation_protein   Finds the LAPALA
nEmptyLines             Number of empty lines in the data
nonzero                 Retrieve the indices of non-zero elements in
                        sparse matrices
normalization_methods   Normalisation
normalizeFunction       Normalisation for QFeatures
output_2_Excel          This function exports a data.frame to a Excel
                        file.
paramshistory           List of metacell tags
pepaTest                PEptide based Protein differential Abundance
                        test
pkgsRequire             Loads packages
plotCompareAssays       Compare two assays
plotJitter              Jitter plot of CC
plotJitter_rCharts      Display a a jitter plot for CC
postHocTest             Post-hoc tests for classic 1-way ANOVA
pushpvalue              Push p-values based on metacell tags
q_metacell              Quantitative metadata vocabulary for entities
samLRT                  Computes a regularized version of the
                        likelihood ratio statistic
separateAdjPval         Computes the adjusted p-values separately on
                        contrast using CP4P
splitAdjacencyMat       splits an adjacency matrix into specific and
                        shared
subR25pept              subR25pept dataset
subR25prot              subR25prot dataset
testAnovaModels         Applies a statistical test on each element of a
                        list of linear models
testDesign              Check the validity of the design
thresholdpval4fdr       Applies p-value adjustment using cp4p on
                        p-values below a given threshold
translatedRandomBeta    Generator of simulated values
wrapperCalibrationPlot
                        Performs a calibration plot on an
                        'SummarizedExperiment' object, calling the
                        'cp4p' package functions.
wrapperClassic1wayAnova
                        Wrapper for One-way Anova statistical test
wrapperDaparImputeMI    Missing values imputation using the LSimpute
                        algorithm.
wrapperImputeMLE        Imputation of peptides having no values in a
                        biological condition.
wrapperImputePA2        Missing values imputation from a
                        'SummarizedExperiment' object
wrapperPirat            Missing values imputation using Pirat
