Tools for the Differential Analysis of Proteins Abundance with R

Documentation for package ‘DAPAR’ version 1.30.6

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-- A --

aggregateIter	xxxx
aggregateIterParallel	xxxx
aggregateMean	Compute the intensity of proteins as the mean of the intensities of their peptides.
AggregateMetacell	Symbolic product of matrices
aggregateSum	Compute the intensity of proteins with the sum of the intensities of their peptides.
aggregateTopn	Compute the intensity of proteins as the sum of the intensities of their n best peptides.
averageIntensities	Average protein/peptide abundances for each condition studied

-- B --

barplotEnrichGO_HC	A barplot that shows the result of a GO enrichment, using the package 'highcharter'
barplotGroupGO_HC	A barplot which shows the result of a GO classification, using the package 'highcharter'
boxPlotD_HC	Builds a boxplot from a dataframe using the package 'highcharter'
BuildAdjacencyMatrix	Function matrix of appartenance group
BuildColumnToProteinDataset	creates a column for the protein dataset after agregation by using the previous peptide dataset.
buildGraph	Display a CC
BuildMetaCell	Builds cells metadata

-- C --

check.conditions	Check if the design is valid
check.design	Check if the design is valid
checkClusterability	xxx
classic1wayAnova	Function to perform a One-way Anova statistical test on a MsnBase dataset
compareNormalizationD_HC	Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'highcharter'
compute_t_tests	xxxxxx
corrMatrixD_HC	Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table.
CountPep	Compute the number of peptides used to aggregate proteins
createMSnset	Creates an object of class 'MSnSet' from text file
CVDistD_HC	Distribution of CV of entities

-- D --

dapar_hc_chart	Customised resetZoomButton of highcharts plots
dapar_hc_ExportMenu	Customised contextual menu of highcharts plots
deleteLinesFromIndices	Delete the lines in the matrix of intensities and the metadata table given their indice.
densityPlotD_HC	Builds a densityplot from a dataframe
diffAnaComputeFDR	Computes the FDR corresponding to the p-values of the differential analysis using
diffAnaGetSignificant	Returns a MSnSet object with only proteins significant after differential analysis.
diffAnaSave	Returns a 'MSnSet' object with the results of the differential analysis performed with 'limma' package.
diffAnaVolcanoplot	Volcanoplot of the differential analysis
diffAnaVolcanoplot_rCharts	Volcanoplot of the differential analysis
display.CC.visNet	Display a CC

-- E --

enrich_GO	Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance.
ExtendPalette	Extends a base-palette of the package RColorBrewer to n colors.

-- F --

finalizeAggregation	Finalizes the aggregation process
findMECBlock	Finds the LAPALA into a 'MSnSet' object
formatLimmaResult	xxxx
formatPHResults	Extract logFC and raw pvalues from multiple post-hoc models summaries
fudge2LRT	Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic

-- G --

get.pep.prot.cc	Build the list of connex composant of the adjacency matrix
GetCC	Returns the contains of the slot processing of an object of class 'MSnSet'
GetColorsForConditions	Builds a complete color palette for the conditions given in argument
GetDetailedNbPeptides	Computes the detailed number of peptides for each protein
GetDetailedNbPeptidesUsed	Computes the detailed number of peptides used for aggregating each protein
getIndicesConditions	Gets the conditions indices.
getIndicesOfLinesToRemove	Get the indices of the lines to delete, based on a prefix string
GetIndices_BasedOnConditions	Search lines which respects request on one or more conditions.
GetIndices_MetacellFiltering	Delete the lines in the matrix of intensities and the metadata table given their indice.
GetIndices_WholeLine	Search lines which respects query on all their elements.
GetIndices_WholeMatrix	Search lines which respects request on one or more conditions.
GetKeyId	xxxx
getListNbValuesInLines	Returns the possible number of values in lines in the data
GetMatAdj	Returns the contains of the slot processing of an object of class 'MSnSet'
GetMetacell	xxxx
GetMetacellTags	List of metacell tags
GetNbPeptidesUsed	Computes the number of peptides used for aggregating each protein
getNumberOf	Number of lines with prefix
getNumberOfEmptyLines	Returns the number of empty lines in the data
getPourcentageOfMV	Percentage of missing values
getProcessingInfo	Returns the contains of the slot processing of an object of class 'MSnSet'
getProteinsStats	Computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two.
getQuantile4Imp	Quantile imputation value definition
GetSoftAvailables	The set of softwares available
getTextForAggregation	Build the text information for the Aggregation process
getTextForAnaDiff	Build the text information for the Aggregation process
getTextForFiltering	Build the text information for the filtering process
getTextForGOAnalysis	Build the text information for the Aggregation process
getTextForHypothesisTest	Build the text information for the hypothesis test process
getTextForNewDataset	Build the text information for a new dataset
getTextForNormalization	Build the text information for the Normalization process
getTextForpeptideImputation	Build the text information for the peptide Imputation process
getTextForproteinImputation	Build the text information for the protein Imputation process
GetTypeofData	xxxx
Get_AllComparisons	Returns list that contains a list of the statistical tests performed with DAPAR and recorded in an object of class 'MSnSet'.
GlobalQuantileAlignment	Normalisation GlobalQuantileAlignement
GOAnalysisSave	Returns an 'MSnSet' object with the results of the GO analysis performed with the functions 'enrichGO' and/or 'groupGO' of the 'clusterProfiler' package.
GraphPepProt	Function to create a histogram that shows the repartition of peptides w.r.t. the proteins
group_GO	Calculates the GO profile of a vector of genes/proteins at a given level of the Gene Ontology

-- H --

hc_logFC_DensityPlot	Density plots of logFC values
hc_mvTypePlot2	Distribution of Observed values with respect to intensity values
heatmapD	This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet'
heatmapForMissingValues	xxx
histPValue_HC	Plots a histogram ov p-values

-- I --

impute.pa2	Missing values imputation from a 'MSnSet' object
inner.aggregate.iter	xxxx
inner.aggregate.topn	xxxx
inner.mean	xxxx
inner.sum	xxxx

-- L --

LH0	xxxxxx
LH0.lm	xxxxxx
LH1	xxxxxx
LH1.lm	xxxxxx
limmaCompleteTest	Computes a hierarchical differential analysis
listSheets	This function returns the list of the sheets names in a Excel file.
LOESS	Normalisation LOESS

-- M --

make.contrast	Builds the contrast matrix
make.design	Builds the design matrix
make.design.1	Builds the design matrix for designs of level 1
make.design.2	Builds the design matrix for designs of level 2
make.design.3	Builds the design matrix for designs of level 3
match.metacell	Similar to the function 'is.na' but focused on the equality with the paramter 'type'.
MeanCentering	Normalisation MeanCentering
metacell.def	Metadata vocabulary for entities
MetaCellFiltering	Filter lines in the matrix of intensities w.r.t. some criteria
MetacellFilteringScope	Lists the metacell scopes for filtering
metacellHisto_HC	Histogram of missing values
metacellPerLinesHistoPerCondition_HC	Bar plot of missing values per lines and per condition
metacellPerLinesHisto_HC	Bar plot of missing values per lines using highcharter
Metacell_DIA_NN	Sets the metacell dataframe for datasets which are from Dia-NN software
Metacell_generic	Sets the metacell dataframe for dataset without information about the origin of identification
Metacell_maxquant	Sets the metacell dataframe
Metacell_proline	Sets the metacell dataframe for datasets which are from Proline software
metacombine	Combine peptide metadata to build protein metadata
mvImage	Heatmap of missing values
my_hc_chart	Customised resetZoomButton of highcharts plots
my_hc_ExportMenu	Customised contextual menu of highcharts plots

-- N --

nonzero	Retrieve the indices of non-zero elements in sparse matrices
normalizeMethods.dapar	List normalization methods with tracking option
NumericalFiltering	Removes lines in the dataset based on numerical conditions.
NumericalgetIndicesOfLinesToRemove	Get the indices of the lines to delete, based on a prefix string

-- P --

pepa.test	PEptide based Protein differential Abundance test
pkgs.require	Loads packages
plotJitter	Jitter plot of CC
plotJitter_rCharts	Display a a jitter plot for CC
plotPCA_Eigen	Plots the eigen values of PCA
plotPCA_Eigen_hc	Plots the eigen values of PCA with the highcharts library
plotPCA_Ind	Plots individuals of PCA
plotPCA_Var	Plots variables of PCA
postHocTest	Post-hoc tests for classic 1-way ANOVA
proportionConRev_HC	Barplot of proportion of contaminants and reverse

-- Q --

QuantileCentering

Normalisation QuantileCentering

-- R --

rbindMSnset	Similar to the function 'rbind' but applies on two subsets of the same 'MSnSet' object.
readExcel	This function reads a sheet of an Excel file and put the data into a data.frame.
reIntroduceMEC	Put back LAPALA into a 'MSnSet' object
removeLines	Removes lines in the dataset based on a prefix string.

-- S --

samLRT	xxxxxx
saveParameters	Saves the parameters of a tool in the pipeline of Prostar
scatterplotEnrichGO_HC	A dotplot that shows the result of a GO enrichment, using the package 'highcharter'
search.metacell.tags	Search pattern in metacell vocabulary
SetCC	Returns the connected components
SetMatAdj	Record the adjacency matrices in a slot of the dataset of class 'MSnSet'
Set_POV_MEC_tags	Sets the MEC tag in the metacell
splitAdjacencyMat	splits an adjacency matrix into specific and shared
StringBasedFiltering	Removes lines in the dataset based on a prefix strings (contaminants, reverse or both).
StringBasedFiltering2	Removes lines in the dataset based on a prefix strings.
SumByColumns	Normalisation SumByColumns
SymFilteringOperators	xxx

-- T --

test.design	Check if xxxxxx
translatedRandomBeta	Generator of simulated values

-- U --

univ_AnnotDbPkg	Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF
UpdateMetacell	Update metacell after imputation

-- V --

violinPlotD	Builds a violinplot from a dataframe
visualizeClusters	Visualize the clusters according to pvalue thresholds
vsn	Normalisation vsn

-- W --

wrapper.compareNormalizationD_HC	Builds a plot from a dataframe
wrapper.corrMatrixD_HC	Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table
wrapper.CVDistD_HC	Distribution of CV of entities
wrapper.dapar.impute.mi	Missing values imputation using the LSimpute algorithm.
wrapper.heatmapD	This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet'
wrapper.impute.detQuant	Wrapper of the function 'impute.detQuant()' for objects of class 'MSnSet'
wrapper.impute.fixedValue	Missing values imputation from a 'MSnSet' object
wrapper.impute.KNN	KNN missing values imputation from a 'MSnSet' object
wrapper.impute.mle	Imputation of peptides having no values in a biological condition.
wrapper.impute.pa	Imputation of peptides having no values in a biological condition.
wrapper.impute.pa2	Missing values imputation from a 'MSnSet' object
wrapper.impute.slsa	Imputation of peptides having no values in a biological condition.
wrapper.mvImage	Heatmap of missing values from a 'MSnSet' object
wrapper.normalizeD	Normalisation
wrapper.pca	Compute the PCA
wrapperCalibrationPlot	Performs a calibration plot on an 'MSnSet' object, calling the 'cp4p' package functions.
wrapperClassic1wayAnova	Wrapper for One-way Anova statistical test
wrapperRunClustering	clustering pipeline of protein/peptide abundance profiles.
write.excel	This function exports a data.frame to a Excel file.
writeMSnsetToCSV	Exports a MSnset dataset into a zip archive containing three zipped CSV files.
writeMSnsetToExcel	This function exports a 'MSnSet' object to a Excel file.