Tools for the Differential Analysis of Proteins Abundance with R


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Documentation for package ‘DAPAR’ version 1.10.4

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

-- 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.

-- C --

compareNormalizationD Builds a plot from a dataframe
compareNormalizationD_HC Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'highcharter'
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
diffAna This function performs a differential analysis on an MSnSet object (adapted from 'limma')
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.
diffAnaLimma Performs differential analysis on an MSnSet object, calling the 'limma' package functions
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
diffAnaWelch Performs a differential analysis on a 'MSnSet' object using the Welch t-test

-- E --

enrich_GO Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance.

-- F --

fudge2LRT Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic

-- G --

getIndicesConditions Gets the conditions indices.
getIndicesOfLinesToRemove Get the indices of the lines to delete, based on a prefix string
getNumberOf Number of lines with prefix
getNumberOfEmptyLines Returns the number of empty lines in the data
getPaletteForLabels Palette for plots in 'DAPAR'
getPaletteForLabels_HC Palette for highcharter plots used in 'DAPAR'
getPaletteForReplicates Palette for plot the replicates in 'DAPAR'
getPaletteForReplicates_HC Palette for highcharter plot the replicates in DAPAR
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
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 --

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'

-- I --

impute.detQuant Deterministic imputation
impute.pa2 Missing values imputation from a 'MSnSet' object

-- L --

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

-- M --

MeanPeptides Compute the intensity of proteins as the mean of the intensities of their peptides.
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
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
mvPerLinesHistoPerCondition_HC Bar plot of missing values per lines and per condition
mvPerLinesHisto_HC Bar plot of missing values per lines using highcharter
mvTypePlot Distribution of missing values with respect to intensity 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
normalizeD Normalisation
normalizeD2 Normalisation

-- P --

pepa.test PEptide based Protein differential Abundance test
pepAgregate Function agregate peptides to proteins
proportionConRev_HC Barplot of proportion of contaminants and reverse

-- R --

readExcel This function reads a sheet of an Excel file and put the data into a data.frame.
removeLines Removes lines in the dataset based on a prefix string.

-- S --

samLRT xxxxxx
scatterplotEnrichGO_HC A dotplot that shows the result of a GO enrichment, using the package 'highcharter'
SumPeptides Compute the intensity of proteins with the sum of the intensities of their peptides.

-- T --

TopnPeptides Compute the intensity of proteins as the sum of the intensities of their n best peptides.
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.boxPlotD Wrapper to the boxplotD function on an object 'MSnSet'
wrapper.boxPlotD_HC Wrapper to the boxplotD_HC function on an object 'MSnSet'
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.densityPlotD Builds a densityplot from an object of class 'MSnSet'
wrapper.densityPlotD_HC Builds a densityplot from an object of class 'MSnSet'
wrapper.diffAnaLimma Performs differential analysis on an MSnSet object, calling the 'limma' package functions
wrapper.diffAnaWelch Performs a differential analysis on a 'MSnSet' object using the Welch t-test
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.pa Imputation of peptides having no values in a biological condition.
wrapper.impute.pa2 Missing values imputation from a 'MSnSet' object
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.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 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.mvTypePlot Distribution of missing values with respect to intensity values from a 'MSnSet' object
wrapper.normalizeD Normalization
wrapper.normalizeD2 Normalisation
wrapper.violinPlotD Wrapper to the violinPlotD function on an object 'MSnSet'
wrapperCalibrationPlot Performs a calibration plot on an 'MSnSet' object, calling the 'cp4p' package functions.
writeMSnsetToExcel This function exports a 'MSnSet' object to a Excel file.