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

aggregateIterxxxx
aggregateIterParallelxxxx
aggregateMeanCompute the intensity of proteins as the mean of the...
AggregateMetacellSymbolic product of matrices
aggregateSumCompute the intensity of proteins with the sum of the...
aggregateTopnCompute the intensity of proteins as the sum of the...
averageIntensitiesAverage protein/peptide abundances for each condition studied
barplotEnrichGO_HCA barplot that shows the result of a GO enrichment, using the...
barplotGroupGO_HCA barplot which shows the result of a GO classification,...
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...
buildGraphDisplay a CC
BuildMetaCellxxxx
checkClusterabilityPrepare the data for subsequent clustering
check.conditionsCheck if the design is valid
check.designCheck if the design is valid
classic1wayAnovaFunction to perform a One-way Anova statistical test on a...
compareNormalizationD_HCBuilds a plot from a dataframe. Same as compareNormalizationD...
compute_t_testsxxxxxx
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
CVDistD_HCDistribution of CV of entities
dapar_hc_chartCustomised resetZoomButton of highcharts plots
dapar_hc_ExportMenuCustomised contextual menu of highcharts plots
deleteLinesFromIndicesDelete the lines in the matrix of intensities and the...
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
display.CC.visNetDisplay a CC
enrich_GOCalculates GO enrichment classes for a given list of...
ExtendPaletteExtends a base-palette of the package RColorBrewer to n...
finalizeAggregationFinalizes the aggregation process
findMECBlockFinds the LAPALA into a 'MSnSet' object
formatLimmaResultxxxx
formatPHResultsExtract logFC and raw pvalues from multiple post-hoc models...
fudge2LRTHeuristic to choose the value of the hyperparameter (fudge...
Get_AllComparisonsReturns list that contains a list of the statistical tests...
GetCCReturns the contains of the slot processing of an object of...
GetColorsForConditionsBuilds a complete color palette for the conditions given in...
GetDetailedNbPeptidesComputes the detailed number of peptides for each protein
GetDetailedNbPeptidesUsedComputes the detailed number of peptides used for aggregating...
GetIndices_BasedOnConditionsSearch lines which respects request on one or more...
getIndicesConditionsGets the conditions indices.
GetIndices_MetacellFilteringDelete the lines in the matrix of intensities and the...
getIndicesOfLinesToRemoveGet the indices of the lines to delete, based on a prefix...
GetIndices_WholeLineSearch lines which respects query on all their elements.
GetIndices_WholeMatrixSearch lines which respects request on one or more...
GetKeyIdxxxx
getListNbValuesInLinesReturns the possible number of values in lines in the data
GetMatAdjReturns the contains of the slot processing of an object of...
GetMetacellxxxx
GetNbPeptidesUsedComputes the number of peptides used for aggregating each...
getNumberOfNumber of lines with prefix
getNumberOfEmptyLinesReturns the number of empty lines in the data
get.pep.prot.ccBuild the list of connex composant of the adjacency matrix
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
GetTypeofDataxxxx
GlobalQuantileAlignmentNormalisation GlobalQuantileAlignement
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...
heatmapForMissingValuesThis function is inspired from the function 'heatmap.2' that...
histPValue_HCPlots a histogram ov p-values
impute.pa2Missing values imputation from a 'MSnSet' object
inner.aggregate.iterxxxx
inner.aggregate.topnxxxx
inner.meanxxxx
inner.sumxxxx
LH0xxxxxx
LH0.lmxxxxxx
LH1xxxxxx
LH1.lmxxxxxx
limmaCompleteTestComputes a hierarchical differential analysis
listSheetsThis function returns the list of the sheets names in a Excel...
LOESSNormalisation LOESS
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
match.metacellSimilar to the function 'is.na' but focused on the equality...
MeanCenteringNormalisation MeanCentering
metacell.defMetadata vocabulary for entities
MetaCellFilteringFilter lines in the matrix of intensities w.r.t. some...
MetacellFilteringScopeLists the metacell scopes for filtering
Metacell_genericSets the metacell dataframe
metacellHisto_HCHistogram of missing values
Metacell_maxquantSets the metacell dataframe
metacellPerLinesHisto_HCBar plot of missing values per lines using highcharter
metacellPerLinesHistoPerCondition_HCBar plot of missing values per lines and per condition
Metacell_prolineSets the metacell dataframe
metacombineCombine peptide metadata to build protein metadata
mvImageHeatmap of missing values
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
normalizeMethods.daparList normalization methods with tracking option
NumericalFilteringRemoves lines in the dataset based on numerical conditions.
NumericalgetIndicesOfLinesToRemoveGet the indices of the lines to delete, based on a prefix...
pepa.testPEptide based Protein differential Abundance test
plotJitterJitter plot of CC
plotJitter_rChartsDisplay a a jitter plot for CC
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
postHocTestPost-hoc tests for classic 1-way ANOVA
proportionConRev_HCBarplot of proportion of contaminants and reverse
QuantileCenteringNormalisation QuantileCentering
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...
search.metacell.tagsSearch pattern in metacell vocabulary
SetCCReturns the connected components
SetMatAdjRecord the adjacency matrices in a slot of the dataset of...
Set_POV_MEC_tagsSets the MEC tag in the metacell
splitAdjacencyMatsplits an adjacency matrix into specific and shared
StringBasedFilteringRemoves lines in the dataset based on a prefix strings...
StringBasedFiltering2Removes lines in the dataset based on a prefix strings.
SumByColumnsNormalisation SumByColumns
SymFilteringOperatorsxxx
test.designCheck if xxxxxx
translatedRandomBetaGenerator of simulated values
univ_AnnotDbPkgReturns the totality of ENTREZ ID (gene id) of an OrgDb...
UpdateMetacellUpdate metacell after imputation
violinPlotDBuilds a violinplot from a dataframe
visualizeClustersVisualize the clusters according to pvalue thresholds
vsnNormalisation vsn
wrapperCalibrationPlotPerforms a calibration plot on an 'MSnSet' object, calling...
wrapperClassic1wayAnovaWrapper for One-way Anova statistical test
wrapper.compareNormalizationD_HCBuilds a plot from a dataframe
wrapper.corrMatrixD_HCDisplays a correlation matrix of the quantitative data of the...
wrapper.CVDistD_HCDistribution of CV of entities
wrapper.dapar.impute.miMissing values imputation using the LSimpute algorithm.
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.mvImageHeatmap of missing values from a 'MSnSet' object
wrapper.normalizeDNormalisation
wrapper.pcaCompute the PCA
wrapperRunClusteringRun a clustering pipeline of protein/peptide abundance...
write.excelThis function exports a data.frame to a Excel file.
writeMSnsetToCSVExports a MSnset dataset into a zip archive containing three...
writeMSnsetToExcelThis function exports a 'MSnSet' object to a Excel file.
samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.