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.

Author
Samuel Wieczorek [cre,aut], Florence Combes [aut], Thomas Burger [aut], Cosmin Lazar [ctb], Alexia Dorffer [ctb]
Date of publication
None
Maintainer
Samuel Wieczorek <samuel.wieczorek@cea.fr>
License
Artistic-2.0
Version
1.6.0

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