Tools for the Differential Analysis of Proteins Abundance with R


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Documentation for package ‘DAPAR’ version 1.0.0

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boxPlotD Builds a boxplot from an object of class 'MSnSet'
corrMatrixD Displays a correlation matrix of the quantitative data of the 'exprs()' table.
createMSnset Creates an object of class 'MSnSet' from text file
densityPlotD Builds a densityplot from an object of class 'MSnSet'
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.
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
getNumberOfEmptyLines Returns the number of empty lines in the data
getPaletteForLabels Palette for plots in DAPAR
getPourcentageOfMV Percentage of missing values
heatmapD This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'
mvFilter 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
mvPerLinesHisto Histogram of missing values per lines
mvPieChart Pie chart of the missing values
mvTypePlot Distribution of missing values with respect to intensity values
normalizeD Normalisation
test Test dataset
testWithoutNA Test dataset
UPSprotx2 UPSprotx2 dataset
varianceDistD Distribution of variance of proteins
writeMSnsetToExcel This function exports a 'MSnSet' object to a Excel file.