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| ASCA.Calculate | ASCA method (ANOVA-simultaneous component analysis) |
| ASCA.DoPermutationTest | Permutation test for ASCA |
| ASCA.GetPowerSet | Determines the power set of the input set. |
| ASCA.GetRowRepeats | Determination of all unique row value combinations |
| ASCA.GetSummary | Summary method for ASCA analyses |
| ASCA.Plot | Plot ASCA results |
| ASCA.PlotLoadings | Loadings plot for a specific factor/interaction of the ASCA |
| ASCA.PlotScores | Score plot for a specific factor or interaction of the ASCA |
| ASCA.PlotScoresPerLevel | ASCA scores plot with projected data. |
| ASCAdata | Example data for ASCA.Calculate |
| ASCAF | Indicator matrix for ASCA example. |
| ASCAX | Data matrix for ASCA example |
| FoM.Calculate | Calculate best fitting Figure of Merit using method by Van Batenburg et al. (2011). |
| FoM.FitBinnedSampleRepeatErrors | Fitting step in Figure of Merit calculation. |
| FoM.GetIdOrderedMatrix | Order the matrix of samples by their ID |
| FoM.OrderAndBinIdByMeans | Bin sample repeats and samples with similar means |
| FoMData | Example data for FoM.Calculate |
| MetStaT.ConcatWithStringPars | Concatenates an array of strings |
| MetStaT.ConvertToNumeric | Converts a matrix of strings to numeric values |
| MetStaT.ConvertToNumericClasses | Convert value-types in an array or matrix (per column) to pre-defined class-values |
| MetStaT.CreateFileFromHeaderMatrix | Writes a matrix to file with column names and optionally row names as well. |
| MetStaT.CreateFileFromHeaderRowMatrix | Writes a matrix to file with row and column names, and optionally a description at the first (top left) data position in the file. |
| MetStaT.ExportDataToFile | Exports the results of supplied R expressions as text files in a single zip package. |
| MetStaT.GetFreqTable | Tabulates the frequency of all unique values. |
| MetStaT.GetPcTuples | Obtain all possible pairs of principal components out of a defined set. |
| MetStaT.KillAllDevices | Kills all currently active plot windows. |
| MetStaT.mldivide | Matrix left hand division using a copy of the 'pracma' package 'mldivide' method. |
| MetStaT.mrdivide | Matrix right hand division using a copy of the 'pracma' package 'mrdivide' method. |
| MetStaT.PlotToFile | Save results of R plotting expressions to files in a zip package. |
| MetStaT.ReadFileToHeaderMatrix | Reads a data file to a matrix. |
| MetStaT.RemoveNaColumns | Removes all columns in a matrix that contain one or more NAs. |
| MetStaT.ScalePip | Centering and scaling function |
| MetStaT.TrimCustom | Limits an input string to a certain length |
| MetStaT.WriteDataObjectToFile | Write data contained within an R object as character output to a file. |
| PCA.Calculate | Adapted version of R's base Principal Component Analysis function (svd) |
| PCA.PlotLoadings | Loadings plot for the results of PCA.Calculate |
| PCA.PlotScores | Score plot for the results of PCA.Calculate. |
| QStat.Calculate | Global test for metabolic pathway differences between conditions |
| QStat.PermutationTest | Accompanying permutation test for QStat.Calculate |
| QStatX | Data matrix for QStat.Calculate example |
| QStatY | Matrix for QStat.Calculate example |
| RevNet.JacobianMethod | Reverse engineering of networks: Penalized Jacobian method |
| RevNet.TimeLaggedMethod | Reverse engineering of networks: Time-lagged correlation method |
| RevNet.ZeroSlopesMethod | Reverse engineering of networks: zero slopes method |
| RevNetJacobian | Example data for RevNetJacobianMethod |
| RevNetTimeLagged | Example data for RevNetTimeLaggedMethod |
| RevNetZeroSlopes | Example data for RevNetZeroSlopesMethod |
| SteadyState | Example data for RevNetJacobianMethod |