Tools for the Differential Analysis of Proteins Abundance with R

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Documentation for package ‘DAPAR’ version 1.20.2

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A B C D E F G H I L M N P R S T U V W

-- A --

addOriginOfValue Sets the OriginOfValues dataframe
aggregateIter xxxx
aggregateIterParallel xxxx
aggregateMean Compute the intensity of proteins as the mean of the intensities of their peptides.
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.

-- 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 Builds a boxplot from a dataframe
boxPlotD_HC Builds a boxplot from a dataframe using the library 'highcharter'
BuildAdjacencyMatrix Function matrix of appartenance group
BuildColumnToProteinDataset creates a column for the protein dataset after agregation by using the previous peptide dataset.
BuildColumnToProteinDataset_par creates a column for the protein dataset after agregation by using the previous peptide dataset.
buildGraph Display a CC

-- C --

check.conditions Check if the design is valid
check.design Check if the design is valid
compareNormalizationD Builds a plot from a dataframe
compareNormalizationD_HC Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'highcharter'
compute.t.tests xxxxxx
corrMatrixD Displays a correlation matrix of the quantitative data of the 'exprs()' table.
corrMatrixD_HC Displays a correlation matrix of the quantitative data of the 'exprs()' table.
CountPep Compute the number of peptides used to aggregate proteins
createMSnset Creates an object of class 'MSnSet' from text file
CVDistD Distribution of CV of entities
CVDistD_HC Distribution of CV of entities

-- D --

deleteLinesFromIndices Delete the lines in the matrix of intensities and the metadata table given their indice.
densityPlotD Builds a densityplot from a dataframe
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.

-- F --

finalizeAggregation Finalizes the aggregation process
findMECBlock Finds the LAPALA into a 'MSnSet' object
formatLimmaResult xxxx
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
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
getListNbValuesInLines Returns the possible number of values in lines in the data
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
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
Get_AllComparisons Returns list that contains a list of the statistical tests performed with DAPAR and recorded in an object of class 'MSnSet'.
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
heatmap.DAPAR This function is inspired from the function 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'. For more information, please refer to the help of the heatmap.2 function.
heatmapD This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'
histPValue_HC Plots a histogram ov p-values

-- I --

impute.detQuant Deterministic imputation
impute.pa2 Missing values imputation from a 'MSnSet' object
inner.aggregate.iter xxxx
inner.aggregate.topn xxxx
inner.mean xxxx
inner.sum xxxx
is.MV Similar to the function 'is.na' but focused on the equality with the missing values in the dataset (type 'POV' and 'MEC')
is.OfType Similar to the function 'is.na' but focused on the equality with the paramter 'type'.

-- 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.

-- 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
mvFilter Filter lines in the matrix of intensities w.r.t. some criteria
mvFilterFromIndices Filter lines in the matrix of intensities w.r.t. some criteria
mvFilterGetIndices Filter lines in the matrix of intensities w.r.t. some criteria
mvHisto Histogram of missing values
mvHisto_HC Histogram of missing values
mvImage Heatmap of missing values
mvPerLinesHisto Bar plot of missing values per lines
mvPerLinesHistoPerCondition Bar plot of missing values per lines and per condition
mvPerLinesHistoPerCondition_HC Bar plot of missing values per lines and per condition
mvPerLinesHisto_HC Bar plot of missing values per lines using highcharter
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
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
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
proportionConRev_HC Barplot of proportion of contaminants and reverse

-- 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'
setMEC Sets the MEC tag in the OriginOfValues
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.

-- 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

-- V --

violinPlotD Builds a violinplot from a dataframe

-- W --

wrapper.compareNormalizationD Builds a plot from a dataframe
wrapper.compareNormalizationD_HC Builds a plot from a dataframe
wrapper.corrMatrixD Displays a correlation matrix of the quantitative data of the 'exprs()' table
wrapper.corrMatrixD_HC Displays a correlation matrix of the quantitative data of the 'exprs()' table
wrapper.CVDistD Distribution of CV of entities
wrapper.CVDistD_HC Distribution of CV of entities
wrapper.dapar.impute.mi Missing values imputation using the LSimpute algorithm.
wrapper.hc_mvTypePlot2 Distribution of observed values with respect to intensity values from a 'MSnSet' object
wrapper.heatmapD This function is a wrapper to 'heatmap.2' that displays quantitative data in the '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.mvHisto Histogram of missing values from a 'MSnSet' object
wrapper.mvHisto_HC Histogram of missing values from a 'MSnSet' object
wrapper.mvImage Heatmap of missing values 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 an object 'MSnSet'
wrapper.mvPerLinesHistoPerCondition_HC Bar plot of missing values per lines and per conditions from an object 'MSnSet'
wrapper.mvPerLinesHisto_HC Histogram of missing values per lines from an object using highcharter 'MSnSet'
wrapper.normalizeD Normalisation
wrapper.pca Compute the PCA
wrapper.t_test_Complete xxxxx
wrapperCalibrationPlot Performs a calibration plot on an 'MSnSet' object, calling the 'cp4p' package functions.
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.