Man pages for mattdneal/FAIMSToolkit
Tools to aid in the analysis of FAIMS data
| boot_auc_folds | Compute bootstraps of the mean ROC |
| calc_mean_roc | Calculate the mean ROC curve from a list of predictors and... |
| checkDrift | Check for FAIMS drift |
| checkFlowRate | Check the minimum flow rates for all the runs in a dataset |
| ClassifierModels | Run a set of classification models on input training, test... |
| compare_auc_bootstrap | Compute a bootstrap of the difference between two ROC curve... |
| convertToArray | Convert FAIMS data to an array |
| CrossValidation | Cross-validation for classification models |
| CrossValRocCurves | Compute ROC objects for the results of a cross validation |
| deleteFAIMSSample | Delete samples from a FAIMS object |
| denoiseFaimsData | Remove background noise from FAIMS data |
| denoiseFaimsData.localCorr | Remove background noise from FAIMS data using local... |
| evidence_for_k | Calculate the Evidence for k |
| FeatureSelection | perform a feature selection using a Wilcoxon rank-sum test |
| findNoiseFaimsData.localCorr | Remove background noise from FAIMS data using local... |
| findNoiseFaimsData.sd | Identify background noise from FAIMS data |
| generateFolds | Generate a division of a data set into folds |
| getNeighbourIndices | Get Neighbour Indices |
| getRocCurve | Return a ROC curve object, given input class probabilities |
| knnMeanDistance | Find mean k-nearest neighbour distance for each sample |
| nKeep | Select the top n features |
| plotFAIMSdata | Plot FAIMS data matrices |
| plotRocCurve | Plot a ROC curve with CI |
| prettyFAIMSPlot | Plot FAIMS data matrices with axes and ion current scale |
| progBarInit | Initialise a progress bar object |
| progBarUpdate | Update a progress bar object |
| ReadInFaimsData | Read in FAIMS data from a list of files |
| ReadInFaimsDirectories | Read in FAIMS files from a set of directories |
| ReadInFaimsDirectoriesAutosampler | Read FAIMS data generated using an autosampler |
| ReadInFaimsDirectoriesMultiFile | Read and combine multiple FAIMS data files per sample |
| runFAIMS | Run a standard analysis given a FAIMS object and class labels |
| runFold | Utility function to create predictions for a given fold and... |
| select_k | Select PCA PCs to retain |
| SGoF | Significant Goodness of Fit |
| threshold | Select features by threshold |
| WaveletTransform | Perform a 1D wavelet transform on a FAIMS data matrix |
| WaveletTransform_2D | Perform a 2D wavelet transform on a FAIMS data matrix |
