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.

Functions

boxPlotD Man page
BuildAdjacencyMatrix Man page
BuildColumnToProteinDataset Man page
compareNormalizationD Man page
corrMatrixD Man page
CountPep Man page
createMSnset Man page
deleteLinesFromIndices Man page
densityPlotD Man page
diffAna Man page
diffAnaComputeFDR Man page
diffAnaGetSignificant Man page
diffAnaLimma Man page
diffAnaSave Man page
diffAnaVolcanoplot Man page
diffAnaWelch Man page
getIndicesConditions Man page
getIndicesOfLinesToRemove Man page
getNumberOf Man page
getNumberOfEmptyLines Man page
getPaletteForLabels Man page
getPaletteForReplicates Man page
getPourcentageOfMV Man page
getProcessingInfo Man page
getProteinsStats Man page
GraphPepProt Man page
heatmapD Man page
heatmap.DAPAR Man page
limmaCompleteTest Man page
MeanPeptides Man page
mvFilter Man page
mvFilterFromIndices Man page
mvFilterGetIndices Man page
mvHisto Man page
mvImage Man page
mvImputation Man page
mvPerLinesHisto Man page
mvPerLinesHistoPerCondition Man page
mvTypePlot Man page
normalizeD Man page
pepAgregate Man page
proportionConRev Man page
removeLines Man page
SumPeptides Man page
test Man page
testWithoutNA Man page
TopnPeptides Man page
UPSpep25 Man page
varianceDistD Man page
violinPlotD Man page
wrapper.boxPlotD Man page
wrapperCalibrationPlot Man page
wrapper.compareNormalizationD Man page
wrapper.corrMatrixD Man page
wrapper.densityPlotD Man page
wrapper.diffAnaLimma Man page
wrapper.diffAnaWelch Man page
wrapper.heatmapD Man page
wrapper.mvHisto Man page
wrapper.mvImage Man page
wrapper.mvImputation Man page
wrapper.mvPerLinesHisto Man page
wrapper.mvPerLinesHistoPerCondition Man page
wrapper.mvTypePlot Man page
wrapper.normalizeD Man page
wrapper.varianceDistD Man page
wrapper.violinPlotD Man page
writeMSnsetToExcel Man page

Files

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.

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