# Tools for the Differential Analysis of Proteins Abundance with R

## Documentation for package ‘DAPAR’ version 1.8.7

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

## Help Pages

boxPlotD | Builds a boxplot from a dataframe
BuildAdjacencyMatrix | Function matrix of appartenance group
BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by using the previous peptide dataset.
compareNormalizationD | Builds a plot from a dataframe
corrMatrixD | Displays a correlation matrix of the quantitative data of the 'exprs()' table.
CountPep | Compute the number of peptides used to aggregate proteins
createMSnset | Creates an object of class 'MSnSet' from text file
CVDistD | Distribution of CV of entities
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
diffAnaVolcanoplot_rCharts | 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.
GraphPepProt | Function to create a histogram that shows the repartition of peptides w.r.t. the proteins
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.pa2 | Missing values imputation from a 'MSnSet' object
limmaCompleteTest | Computes a hierarchical differential analysis
MeanPeptides | Compute the intensity of proteins as the mean of the intensities of their peptides.
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
normalizeD2 | 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.
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.
translatedRandomBeta | xxxxxxx
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.CVDistD | Distribution of CV of entities
wrapper.dapar.impute.mi | Missing values imputation using the LSimpute algorithm.
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.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.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 | 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.