boxPlotD |
Builds a boxplot from an object of class 'MSnSet' |
corrMatrixD |
Displays a correlation matrix of the quantitative data of the 'exprs()' table. |
createMSnset |
Creates an object of class 'MSnSet' from text file |
densityPlotD |
Builds a densityplot from an object of class 'MSnSet' |
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. |
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 |
getNumberOfEmptyLines |
Returns the number of empty lines in the data |
getPaletteForLabels |
Palette for plots in DAPAR |
getPourcentageOfMV |
Percentage of missing values |
heatmapD |
This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet' |
mvFilter |
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 |
mvPerLinesHisto |
Histogram of missing values per lines |
mvPieChart |
Pie chart of the missing values |
mvTypePlot |
Distribution of missing values with respect to intensity values |
normalizeD |
Normalisation |
test |
Test dataset |
testWithoutNA |
Test dataset |
UPSprotx2 |
UPSprotx2 dataset |
varianceDistD |
Distribution of variance of proteins |
writeMSnsetToExcel |
This function exports a 'MSnSet' object to a Excel file. |