Tools for the Differential Analysis of Proteins Abundance with R


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Documentation for package ‘DAPAR’ version 1.6.0

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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
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.
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'
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
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.
test Test dataset
testWithoutNA Test dataset
TopnPeptides Compute the intensity of proteins as the sum of the intensities of their n best peptides.
UPSpep25 UPSpep25 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.