boxPlotD | Builds a boxplot from a dataframe |
BuildAdjacencyMatrix | Function matrix of appartenance group |
BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by using the previous peptide dataset. |
BuildSparseAdjacencyMatrix | Function matrix of appartenance group |
compareNormalizationD | Builds a plot from a dataframe |
corrMatrixD | 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 |
deleteLinesFromIndices | Delete the lines in the matrix of intensities and the metadata table given their indice. |
densityPlotD | 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 |
diffAnaWelch | Performs a differential analysis on a 'MSnSet' object using the Welch t-test |
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 |
getPaletteForReplicates | Palette for 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. |
GraphPepProt | Function to create a histogram that shows the repartition of peptides w.r.t. the proteins |
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' |
limmaCompleteTest | Computes a hierarchical differential analysis |
MeanPeptides | Compute the intensity of proteins as the mean of the intensities of their peptides. |
MeanPeptidesSpeedUp | 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 |
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 |
mvTypePlot | Distribution of missing values with respect to intensity values |
normalizeD | Normalisation |
pepAgregate | Function agregate peptides to proteins |
pepAgregateSpeedUp | Function agregate peptides to proteins |
proportionConRev | Barplot of proportion of contaminants and reverse |
removeLines | Removes lines in the dataset based on a prefix string. |
SumPeptides | Compute the intensity of proteins with the sum of the intensities of their peptides. |
SumPeptidesSpeedUp | Compute the intensity of proteins with the sum of the intensities of their peptides. |
test | Test dataset |
testWithoutNA | Test dataset |
topMaxUsingPartialSortIndices | Function to return the indices of the n higher values in the vector |
TopnPeptides | Compute the intensity of proteins as the sum of the intensities of their n best peptides. |
UPSpep25 | UPSpep25 dataset |
varianceDistD | Distribution of variance of proteins |
wrapper.boxPlotD | Wrapper to the boxplotD function on an object 'MSnSet' |
wrapper.compareNormalizationD | Builds a plot from a dataframe |
wrapper.corrMatrixD | Displays a correlation matrix of the quantitative data of the 'exprs()' table |
wrapper.densityPlotD | 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.mvHisto | 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.mvTypePlot | Distribution of missing values with respect to intensity values from a 'MSnSet' object |
wrapper.normalizeD | Normalisation |
wrapper.varianceDistD | Distribution of variance of proteins |
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. |