DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

This package contains a collection of functions for the visualisation and the statistical analysis of proteomic data.

AuthorSamuel Wieczorek [cre,aut], Florence Combes [aut], Thomas Burger [aut], Cosmin Lazar [ctb], Alexia Dorffer [ctb]
Date of publicationNone
MaintainerSamuel Wieczorek <samuel.wieczorek@cea.fr>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Man 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...

compareNormalizationD: Builds a plot from a dataframe

corrMatrixD: Displays a correlation matrix of the quantitative data of the...

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...

densityPlotD: Builds a densityplot from a dataframe

diffAna: This function performs a differential analysis on an MSnSet...

diffAnaComputeFDR: Computes the FDR corresponding to the p-values of the...

diffAnaGetSignificant: Returns a MSnSet object with only proteins significant after...

diffAnaLimma: Performs differential analysis on an MSnSet object, calling...

diffAnaSave: Returns a 'MSnSet' object with the results of the...

diffAnaVolcanoplot: Volcanoplot of the differential analysis

diffAnaWelch: Performs a differential analysis on a 'MSnSet' object using...

getIndicesConditions: Gets the conditions indices.

getIndicesOfLinesToRemove: Get the indices of the lines to delete, based on a prefix...

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...

getProteinsStats: computes the number of proteins that are only defined by...

GraphPepProt: Function to create a histogram that shows the repartition of...

heatmapD: This function is a wrapper to 'heatmap.2' that displays...

heatmap.DAPAR: This function is inspired from the function 'heatmap.2' that...

limmaCompleteTest: Computes a hierarchical differential analysis

MeanPeptides: Compute the intensity of proteins as the mean of the...

mvFilter: Filter lines in the matrix of intensities w.r.t. some...

mvFilterFromIndices: Filter lines in the matrix of intensities w.r.t. some...

mvFilterGetIndices: Filter lines in the matrix of intensities w.r.t. some...

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...

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...

test: Test dataset

testWithoutNA: Test dataset

TopnPeptides: Compute the intensity of proteins as the sum of the...

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'

wrapperCalibrationPlot: Performs a calibration plot on an 'MSnSet' object, calling...

wrapper.compareNormalizationD: Builds a plot from a dataframe

wrapper.corrMatrixD: Displays a correlation matrix of the quantitative data of the...

wrapper.densityPlotD: Builds a densityplot from an object of class 'MSnSet'

wrapper.diffAnaLimma: Performs differential analysis on an MSnSet object, calling...

wrapper.diffAnaWelch: Performs a differential analysis on a 'MSnSet' object using...

wrapper.heatmapD: This function is a wrapper to 'heatmap.2' that displays...

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...

wrapper.mvTypePlot: Distribution of missing values with respect to intensity...

wrapper.normalizeD: Normalisation

wrapper.varianceDistD: Distribution of variance of proteins

wrapper.violinPlotD: Wrapper to the violinPlotD function on an object 'MSnSet'

writeMSnsetToExcel: This function exports a 'MSnSet' object to a Excel file.

Files in this package

DAPAR/.BBSoptions
DAPAR/DESCRIPTION
DAPAR/NAMESPACE
DAPAR/NEWS
DAPAR/R
DAPAR/R/DescriptiveStats.R DAPAR/R/DiffAnalysis.R DAPAR/R/agregation.R DAPAR/R/doc-data.R DAPAR/R/inOutFiles.R DAPAR/R/limmaAnalysis.R DAPAR/R/missingValuesFilter.R DAPAR/R/missingValuesImputation.R DAPAR/R/missingValuesPlots.R DAPAR/R/normalize.R DAPAR/R/utils.R DAPAR/R/volcanoPlot.R
DAPAR/build
DAPAR/build/vignette.rds
DAPAR/data
DAPAR/data/UPSpep25.RData
DAPAR/data/datalist
DAPAR/data/test.RData
DAPAR/data/testWithoutNA.RData
DAPAR/inst
DAPAR/inst/CITATION
DAPAR/inst/NEWS
DAPAR/inst/doc
DAPAR/inst/doc/Prostar_UserManual.R
DAPAR/inst/doc/Prostar_UserManual.Rnw
DAPAR/inst/doc/Prostar_UserManual.pdf
DAPAR/inst/doc/UPSprotx2.Rnw
DAPAR/inst/doc/UPSprotx2.pdf
DAPAR/inst/doc/intro.Rnw
DAPAR/inst/doc/intro.pdf
DAPAR/inst/extdata
DAPAR/inst/extdata/UPSpep25.txt
DAPAR/inst/extdata/UPSprotx2.MSnset
DAPAR/inst/extdata/prot10.txt
DAPAR/inst/extdata/samples.txt
DAPAR/inst/extdata/samples_prot10.txt
DAPAR/man
DAPAR/man/BuildAdjacencyMatrix.Rd DAPAR/man/BuildColumnToProteinDataset.Rd DAPAR/man/CountPep.Rd DAPAR/man/GraphPepProt.Rd DAPAR/man/MeanPeptides.Rd DAPAR/man/SumPeptides.Rd DAPAR/man/TopnPeptides.Rd DAPAR/man/UPSpep25.Rd DAPAR/man/boxPlotD.Rd DAPAR/man/compareNormalizationD.Rd DAPAR/man/corrMatrixD.Rd DAPAR/man/createMSnset.Rd DAPAR/man/deleteLinesFromIndices.Rd DAPAR/man/densityPlotD.Rd DAPAR/man/diffAna.Rd DAPAR/man/diffAnaComputeFDR.Rd DAPAR/man/diffAnaGetSignificant.Rd DAPAR/man/diffAnaLimma.Rd DAPAR/man/diffAnaSave.Rd DAPAR/man/diffAnaVolcanoplot.Rd DAPAR/man/diffAnaWelch.Rd DAPAR/man/getIndicesConditions.Rd DAPAR/man/getIndicesOfLinesToRemove.Rd DAPAR/man/getNumberOf.Rd DAPAR/man/getNumberOfEmptyLines.Rd DAPAR/man/getPaletteForLabels.Rd DAPAR/man/getPaletteForReplicates.Rd DAPAR/man/getPourcentageOfMV.Rd DAPAR/man/getProcessingInfo.Rd DAPAR/man/getProteinsStats.Rd DAPAR/man/heatmap.DAPAR.Rd DAPAR/man/heatmapD.Rd DAPAR/man/limmaCompleteTest.Rd DAPAR/man/mvFilter.Rd DAPAR/man/mvFilterFromIndices.Rd DAPAR/man/mvFilterGetIndices.Rd DAPAR/man/mvHisto.Rd DAPAR/man/mvImage.Rd DAPAR/man/mvImputation.Rd DAPAR/man/mvPerLinesHisto.Rd DAPAR/man/mvPerLinesHistoPerCondition.Rd DAPAR/man/mvTypePlot.Rd DAPAR/man/normalizeD.Rd DAPAR/man/pepAgregate.Rd DAPAR/man/proportionConRev.Rd DAPAR/man/removeLines.Rd DAPAR/man/test.Rd DAPAR/man/testWithoutNA.Rd DAPAR/man/varianceDistD.Rd DAPAR/man/violinPlotD.Rd DAPAR/man/wrapper.boxPlotD.Rd DAPAR/man/wrapper.compareNormalizationD.Rd DAPAR/man/wrapper.corrMatrixD.Rd DAPAR/man/wrapper.densityPlotD.Rd DAPAR/man/wrapper.diffAnaLimma.Rd DAPAR/man/wrapper.diffAnaWelch.Rd DAPAR/man/wrapper.heatmapD.Rd DAPAR/man/wrapper.mvHisto.Rd DAPAR/man/wrapper.mvImage.Rd DAPAR/man/wrapper.mvImputation.Rd DAPAR/man/wrapper.mvPerLinesHisto.Rd DAPAR/man/wrapper.mvPerLinesHistoPerCondition.Rd DAPAR/man/wrapper.mvTypePlot.Rd DAPAR/man/wrapper.normalizeD.Rd DAPAR/man/wrapper.varianceDistD.Rd DAPAR/man/wrapper.violinPlotD.Rd DAPAR/man/wrapperCalibrationPlot.Rd DAPAR/man/writeMSnsetToExcel.Rd
DAPAR/tests
DAPAR/tests/testthat
DAPAR/tests/testthat.R
DAPAR/tests/testthat/test_agregation.R
DAPAR/tests/testthat/test_differentialAnalysis.R
DAPAR/tests/testthat/test_mvFilter.R
DAPAR/tests/testthat/test_normalisation.R
DAPAR/vignettes
DAPAR/vignettes/Prostar_UserManual.Rnw
DAPAR/vignettes/UPSprotx2.Rnw
DAPAR/vignettes/images
DAPAR/vignettes/images/Rcode.png
DAPAR/vignettes/images/agregation1.png
DAPAR/vignettes/images/agregation2.png
DAPAR/vignettes/images/anaDiff1.png
DAPAR/vignettes/images/anaDiff2.png
DAPAR/vignettes/images/anaDiff3.png
DAPAR/vignettes/images/anaDiff4.png
DAPAR/vignettes/images/convert_convert.png
DAPAR/vignettes/images/convert_dataID.png
DAPAR/vignettes/images/convert_exp_featdata.png
DAPAR/vignettes/images/convert_sampledata.png
DAPAR/vignettes/images/convert_selectfile.png
DAPAR/vignettes/images/defaultProstar1.png
DAPAR/vignettes/images/demomode.png
DAPAR/vignettes/images/desc_boxplot.png
DAPAR/vignettes/images/desc_corrmatrix.png
DAPAR/vignettes/images/desc_density.png
DAPAR/vignettes/images/desc_fdata.png
DAPAR/vignettes/images/desc_heatmap.png
DAPAR/vignettes/images/desc_missValues.png
DAPAR/vignettes/images/desc_pdata.png
DAPAR/vignettes/images/desc_quantiData.png
DAPAR/vignettes/images/desc_varDist.png
DAPAR/vignettes/images/desc_violinplot.png
DAPAR/vignettes/images/export.png
DAPAR/vignettes/images/filter1.png
DAPAR/vignettes/images/filter2.png
DAPAR/vignettes/images/filter3.png
DAPAR/vignettes/images/imputation.png
DAPAR/vignettes/images/logSession.png
DAPAR/vignettes/images/normalisation.png
DAPAR/vignettes/images/open_msnset.png
DAPAR/vignettes/intro.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.