B C D E F G H I L M N P R S T U V W
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. |
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 |
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 |
enrich_GO | Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance. |
fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic |
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 |
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' |
impute.detQuant | Deterministic imputation |
impute.pa2 | Missing values imputation from a 'MSnSet' object |
LH0 | xxxxxx |
LH1 | xxxxxx |
limmaCompleteTest | Computes a hierarchical differential analysis |
listSheets | This function returns the list of the sheets names in a Excel file. |
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 |
nonzero | Retrieve the indices of non-zero elements in sparse matrices |
normalizeD | Normalisation |
normalizeD2 | Normalisation |
pepa.test | PEptide based Protein differential Abundance test |
pepAgregate | Function agregate peptides to proteins |
proportionConRev_HC | Barplot of proportion of contaminants and reverse |
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. |
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. |
TopnPeptides | Compute the intensity of proteins as the sum of the intensities of their n best peptides. |
translatedRandomBeta | Generator of simulated values |
univ_AnnotDbPkg | Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF |
violinPlotD | Builds a violinplot from a dataframe |
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. |