Man pages for marioni-group/MethylPipeR
MethylPipeR
| assignTrainingFolds | Assigns each row in the input data a fold number randomly... |
| beginPipelineRun | This function is for an older version of MethylPipeR and is... |
| calculateMetricsBinaryClassifier | This function is for an older version of MethylPipeR and is... |
| checkMatrixOrDF | Title |
| checkMethod | Title |
| checkMethodPackageInstalled | Title |
| checkNA | Title |
| checkType | Title |
| createClassWeights | createClassWeights |
| endPipelineRun | This function is for an older version of MethylPipeR and is... |
| fitBARTSurvival | fitBARTSurvival |
| fitCoxModel | This function is for an older version of MethylPipeR and is... |
| fitCoxPH | Fit coxph model with a predictor variable and a set of... |
| fitLogisticModel | This function is for an older version of MethylPipeR and is... |
| fitMPRModel | fitMPRModel |
| fitMPRModelCV | fitMPRModelCV |
| fitMPRModelIncremental | fitMPRModelIncremental |
| getBalancedCVFoldIDs | For binary outcomes. Create a vector of (integer) fold... |
| getGroupCVFoldIDs | Given a vector of group IDs 'groups', returns a vector where... |
| getNonZeroCoefficients | This function is for an older version of MethylPipeR and is... |
| incrementalTest | incrementalTest Fits incremental logistic models (a null... |
| initLogs | To be called at the beginning of a MethylPipeR session.... |
| loadData | Load data from a file. Currently supports .rds and .csv files |
| logSessionLines | Writes lines to the session log. |
| multipleROC | multipleROC Plot multiple ROC or PRROC curves with associated... |
| plotMPRIncrementalModelConfusionMatrix | Plots confusion matrix metrics (true/false... |
| plotMPRIncrementalModelROC | Title |
| plotSingleVariableDensity | plotSingleVariableDensity This old-format function is... |
| plotVariableByGroupDensity | plotVariableByGroupDensity |
| predictCoxModel | This function is for an older version of MethylPipeR and is... |
| predictLogisticModel | This function is for an older version of MethylPipeR and is... |
| predictMPRModel | predictMPRModel |
| removeDeathsFromControls | removeDeathsFromControls |
| rfCV | rfCV |
| saveMPRModelObject | Saves a MPRModel object to the logging folder. |
| thresholdTTE | thresholdTTE |
| trainAndTestRF | trainAndTestRF |
