Man pages for DAPAR
Tools for the Differential Analysis of Proteins Abundance with R

addOriginOfValueSets the OriginOfValues dataframe
aggregateIterxxxx
aggregateIterParallelxxxx
aggregateMeanCompute the intensity of proteins as the mean of the...
aggregateSumCompute the intensity of proteins with the sum of the...
aggregateTopnCompute the intensity of proteins as the sum of the...
barplotEnrichGO_HCA barplot that shows the result of a GO enrichment, using the...
barplotGroupGO_HCA barplot which shows the result of a GO classification,...
boxPlotDBuilds a boxplot from a dataframe
boxPlotD_HCBuilds a boxplot from a dataframe using the library...
BuildAdjacencyMatrixFunction matrix of appartenance group
BuildColumnToProteinDatasetcreates a column for the protein dataset after agregation by...
BuildColumnToProteinDataset_parcreates a column for the protein dataset after agregation by...
check.conditionsCheck if the design is valid
check.designCheck if the design is valid
compareNormalizationDBuilds a plot from a dataframe
compareNormalizationD_HCBuilds a plot from a dataframe. Same as compareNormalizationD...
compute.t.testsxxxxxx
corrMatrixDDisplays a correlation matrix of the quantitative data of the...
corrMatrixD_HCDisplays a correlation matrix of the quantitative data of the...
CountPepCompute the number of peptides used to aggregate proteins
createMSnsetCreates an object of class 'MSnSet' from text file
CVDistDDistribution of CV of entities
CVDistD_HCDistribution of CV of entities
deleteLinesFromIndicesDelete the lines in the matrix of intensities and the...
densityPlotDBuilds a densityplot from a dataframe
densityPlotD_HCBuilds a densityplot from a dataframe
diffAnaComputeFDRComputes the FDR corresponding to the p-values of the...
diffAnaGetSignificantReturns a MSnSet object with only proteins significant after...
diffAnaSaveReturns a 'MSnSet' object with the results of the...
diffAnaVolcanoplotVolcanoplot of the differential analysis
diffAnaVolcanoplot_rChartsVolcanoplot of the differential analysis
enrich_GOCalculates GO enrichment classes for a given list of...
finalizeAggregationFinalizes the aggregation process
findMECBlockFinds the LAPALA into a 'MSnSet' object
formatLimmaResultxxxx
fudge2LRTHeuristic to choose the value of the hyperparameter (fudge...
getIndicesConditionsGets the conditions indices.
getIndicesOfLinesToRemoveGet the indices of the lines to delete, based on a prefix...
getListNbValuesInLinesReturns the possible number of values in lines in the data
GetNbPeptidesUsedComputes the number of peptides used for aggregating each...
getNumberOfNumber of lines with prefix
getNumberOfEmptyLinesReturns the number of empty lines in the data
getPourcentageOfMVPercentage of missing values
getProcessingInfoReturns the contains of the slot processing of an object of...
getProteinsStatsComputes the number of proteins that are only defined by...
getQuantile4ImpQuantile imputation value definition
getTextForAggregationBuild the text information for the Aggregation process
getTextForAnaDiffBuild the text information for the Aggregation process
getTextForFilteringBuild the text information for the filtering process
getTextForGOAnalysisBuild the text information for the Aggregation process
getTextForHypothesisTestBuild the text information for the hypothesis test process
getTextForNewDatasetBuild the text information for a new dataset
getTextForNormalizationBuild the text information for the Normalization process
getTextForpeptideImputationBuild the text information for the peptide Imputation process
getTextForproteinImputationBuild the text information for the protein Imputation process
GOAnalysisSaveReturns an 'MSnSet' object with the results of the GO...
GraphPepProtFunction to create a histogram that shows the repartition of...
group_GOCalculates the GO profile of a vector of genes/proteins at a...
hc_logFC_DensityPlotDensity plots of logFC values
hc_mvTypePlot2Distribution of Observed values with respect to intensity...
heatmapDThis function is a wrapper to 'heatmap.2' that displays...
heatmap.DAPARThis function is inspired from the function 'heatmap.2' that...
impute.detQuantDeterministic imputation
impute.pa2Missing values imputation from a 'MSnSet' object
inner.aggregate.iterxxxx
inner.aggregate.topnxxxx
inner.meanxxxx
inner.sumxxxx
is.MVSimilar to the function 'is.na' but focused on the equality...
is.OfTypeSimilar to the function 'is.na' but focused on the equality...
LH0xxxxxx
LH0.lmxxxxxx
LH1xxxxxx
LH1.lmxxxxxx
limmaCompleteTestComputes a hierarchical differential analysis
listSheetsThis function returns the list of the sheets names in a Excel...
make.contrastBuilds the contrast matrix
make.designBuilds the design matrix
make.design.1Builds the design matrix for designs of level 1
make.design.2Builds the design matrix for designs of level 2
make.design.3Builds the design matrix for designs of level 3
mvFilterFilter lines in the matrix of intensities w.r.t. some...
mvFilterFromIndicesFilter lines in the matrix of intensities w.r.t. some...
mvFilterGetIndicesFilter lines in the matrix of intensities w.r.t. some...
mvHistoHistogram of missing values
mvHisto_HCHistogram of missing values
mvImageHeatmap of missing values
mvPerLinesHistoBar plot of missing values per lines
mvPerLinesHisto_HCBar plot of missing values per lines using highcharter
mvPerLinesHistoPerConditionBar plot of missing values per lines and per condition
mvPerLinesHistoPerCondition_HCBar plot of missing values per lines and per condition
my_hc_chartCustomised resetZoomButton of highcharts plots
my_hc_ExportMenuCustomised contextual menu of highcharts plots
nonzeroRetrieve the indices of non-zero elements in sparse matrices
pepa.testPEptide based Protein differential Abundance test
plotPCA_EigenPlots the eigen values of PCA
plotPCA_Eigen_hcPlots the eigen values of PCA with the highcharts library
plotPCA_IndPlots individuals of PCA
plotPCA_VarPlots variables of PCA
proportionConRev_HCBarplot of proportion of contaminants and reverse
rbindMSnsetSimilar to the function 'rbind' but applies on two subsets of...
readExcelThis function reads a sheet of an Excel file and put the data...
reIntroduceMECPut back LAPALA into a 'MSnSet' object
removeLinesRemoves lines in the dataset based on a prefix string.
samLRTxxxxxx
saveParametersSaves the parameters of a tool in the pipeline of Prostar
scatterplotEnrichGO_HCA dotplot that shows the result of a GO enrichment, using the...
setMECSets the MEC tag in the OriginOfValues
StringBasedFilteringRemoves lines in the dataset based on a prefix strings...
StringBasedFiltering2Removes lines in the dataset based on a prefix strings.
test.designCheck if xxxxxx
translatedRandomBetaGenerator of simulated values
univ_AnnotDbPkgReturns the totality of ENTREZ ID (gene id) of an OrgDb...
violinPlotDBuilds a violinplot from a dataframe
wrapperCalibrationPlotPerforms a calibration plot on an 'MSnSet' object, calling...
wrapper.compareNormalizationDBuilds a plot from a dataframe
wrapper.compareNormalizationD_HCBuilds a plot from a dataframe
wrapper.corrMatrixDDisplays a correlation matrix of the quantitative data of the...
wrapper.corrMatrixD_HCDisplays a correlation matrix of the quantitative data of the...
wrapper.CVDistDDistribution of CV of entities
wrapper.CVDistD_HCDistribution of CV of entities
wrapper.dapar.impute.miMissing values imputation using the LSimpute algorithm.
wrapper.hc_mvTypePlot2Distribution of observed values with respect to intensity...
wrapper.heatmapDThis function is a wrapper to 'heatmap.2' that displays...
wrapper.impute.detQuantWrapper of the function 'impute.detQuant' for objects of...
wrapper.impute.fixedValueMissing values imputation from a 'MSnSet' object
wrapper.impute.KNNKNN missing values imputation from a 'MSnSet' object
wrapper.impute.mleImputation of peptides having no values in a biological...
wrapper.impute.paImputation of peptides having no values in a biological...
wrapper.impute.pa2Missing values imputation from a 'MSnSet' object
wrapper.impute.slsaImputation of peptides having no values in a biological...
wrapper.mvHistoHistogram of missing values from a 'MSnSet' object
wrapper.mvHisto_HCHistogram of missing values from a 'MSnSet' object
wrapper.mvImageHeatmap of missing values from a 'MSnSet' object
wrapper.mvPerLinesHistoHistogram of missing values per lines from an object 'MSnSet'
wrapper.mvPerLinesHisto_HCHistogram of missing values per lines from an object using...
wrapper.mvPerLinesHistoPerConditionBar plot of missing values per lines and per conditions from...
wrapper.mvPerLinesHistoPerCondition_HCBar plot of missing values per lines and per conditions from...
wrapper.normalizeDNormalisation
wrapper.pcaCompute the PCA
wrapper.t_test_Completexxxxx
writeMSnsetToCSVExports a MSnset dataset into a zip archive containing three...
writeMSnsetToExcelThis function exports a 'MSnSet' object to a Excel file.
DAPAR documentation built on Dec. 14, 2018, 6 p.m.