# Tools for the Differential Analysis of Proteins Abundance with R

## Documentation for package ‘DAPAR’ version 1.28.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P Q R S T U V W

## -- A --

aggregateIter | xxxx
aggregateIterParallel | xxxx
aggregateMean | Compute the intensity of proteins as the mean of the intensities of their peptides.
AggregateMetacell | Symbolic product of matrices
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

## -- B --

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 package '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
BuildMetaCell | xxxx

## -- C --

check.conditions | Check if the design is valid
check.design | Check if the design is valid
checkClusterability | xxx
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 'Biobase::exprs()' table.
CountPep | Compute the number of peptides used to aggregate proteins
createMSnset | Creates an object of class 'MSnSet' from text file
CVDistD_HC | Distribution of CV of entities

## -- D --

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_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

## -- E --

enrich_GO | Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance.
ExtendPalette | Extends a base-palette of the package RColorBrewer to n colors.

## -- F --

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

## -- G --

get.pep.prot.cc | Build the list of connex composant of the adjacency matrix
GetCC | Returns the contains of the slot processing of an object of class 'MSnSet'
GetColorsForConditions | Builds a complete color palette for the conditions given in argument
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
GetIndices_BasedOnConditions | Search lines which respects request on one or more conditions.
GetIndices_MetacellFiltering | Delete the lines in the matrix of intensities and the metadata table given their indice.
GetIndices_WholeLine | Search lines which respects query on all their elements.
GetIndices_WholeMatrix | Search lines which respects request on one or more conditions.
GetKeyId | xxxx
getListNbValuesInLines | Returns the possible number of values in lines in the data
GetMatAdj | Returns the contains of the slot processing of an object of class 'MSnSet'
GetMetacell | xxxx
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
GetTypeofData | xxxx
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

## -- H --

hc_logFC_DensityPlot | Density plots of logFC values
hc_mvTypePlot2 | Distribution of Observed values with respect to intensity values
heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet'
heatmapForMissingValues | xxx
histPValue_HC | Plots a histogram ov p-values

## -- I --

impute.pa2 | Missing values imputation from a 'MSnSet' object
inner.aggregate.iter | xxxx
inner.aggregate.topn | xxxx
inner.mean | xxxx
inner.sum | xxxx

## -- L --

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

## -- M --

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
match.metacell | Similar to the function 'is.na' but focused on the equality with the paramter 'type'.
MeanCentering | Normalisation MeanCentering
metacell.def | Metadata vocabulary for entities
MetaCellFiltering | Filter lines in the matrix of intensities w.r.t. some criteria
MetacellFilteringScope | Lists the metacell scopes for filtering
metacellHisto_HC | Histogram of missing values
metacellPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per condition
metacellPerLinesHisto_HC | Bar plot of missing values per lines using highcharter
Metacell_generic | Sets the metacell dataframe
Metacell_maxquant | Sets the metacell dataframe
Metacell_proline | Sets the metacell dataframe
metacombine | Combine peptide metadata to build protein metadata
mvImage | Heatmap of missing values
my_hc_chart | Customised resetZoomButton of highcharts plots
my_hc_ExportMenu | Customised contextual menu of highcharts plots

## -- N --

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

## -- P --

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

## -- Q --

QuantileCentering | Normalisation QuantileCentering

## -- R --

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.

## -- S --

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'
search.metacell.tags | Search pattern in metacell vocabulary
SetCC | Returns the connected components
SetMatAdj | Record the adjacency matrices in a slot of the dataset of class 'MSnSet'
Set_POV_MEC_tags | Sets the MEC tag in the metacell
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
SymFilteringOperators | xxx

## -- T --

test.design | Check if xxxxxx
translatedRandomBeta | Generator of simulated values

## -- U --

univ_AnnotDbPkg | Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF
UpdateMetacell | Update metacell after imputation

## -- V --

violinPlotD | Builds a violinplot from a dataframe
visualizeClusters | Visualize the clusters according to pvalue thresholds
vsn | Normalisation vsn

## -- W --

wrapper.compareNormalizationD_HC | Builds a plot from a dataframe
wrapper.corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table
wrapper.CVDistD_HC | Distribution of CV of entities
wrapper.dapar.impute.mi | Missing values imputation using the LSimpute algorithm.
wrapper.heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::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.mvImage | Heatmap of missing values from a 'MSnSet' object
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 | clustering pipeline of protein/peptide abundance profiles.
write.excel | This function exports a data.frame to a Excel file.
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.