Man pages for marchion/switchBox
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
| KTSP.Classify | Function to classify samples using a KTSP classifier. |
| KTSP.Train | Funtion for training the K-TSP classifier. |
| matTesting | Gene expression matrix for test set data |
| matTraining | Gene expression matrix for training set data |
| SWAP.Calculate.BasicTSPScores | Function to calculate basic TSP scores. |
| SWAP.CalculateScores | Function to calculate the pair-wise scores with any given... |
| SWAP.CalculateSignedScore | Function to calculate the pair-wise scores. |
| SWAP.Calculate.SignedTSPScores | Function to calculate signed TSP scores. |
| SWAP.Filter.Wilcoxon | Statistical feature filtering based on Wilcoxon test on the... |
| SWAP.GetKTSP.PredictionStats | Function for computing various performance measures related... |
| SWAP.GetKTSP.Result | Function for prediction followed by computing various... |
| SWAP.GetKTSP.TrainTestResults | Trains a kTSP on given training data and provides performance... |
| SWAP.Kby.Measurement | K selection for a kTSP classifier. |
| SWAP.Kby.Ttest | K selection for a kTSP classifier. |
| SWAP.KTSP.Classify | Function to classify samples using a KTSP classifier. |
| SWAP.KTSP.CV | Performs k-fold cross validation. |
| SWAP.KTSP.LOO | Performs leave one out cross validation. |
| SWAP.KTSP.Statistic | Function computing TSP votes (comparisons) and combine their... |
| SWAP.KTSP.Train | Deprecated function for training the K-TSP classifier. |
| SWAP.MakeTSPTable | Make a table of TSPs in order of TSP score. |
| SWAP.PlotKTSP.GenePairBoxplot | Plots a feature pair as boxplots. |
| SWAP.PlotKTSP.GenePairClassesBoxplot | Plots a feature pair as seperated by class as boxplots. |
| SWAP.PlotKTSP.GenePairScatter | Make a scatter plot of two features. |
| SWAP.PlotKTSP.Genes | Plot features seperated by phenotype |
| SWAP.PlotKTSP.TrainTestROC | Plots an ROC curve for training and testing results. |
| SWAP.PlotKTSP.Votes | Plots a heatmap of k-TSP votes. |
| SWAP.Train.1TSP | Function for training the 1-TSP classifier. |
| SWAP.Train.KTSP | Function for training the K-TSP classifier. |
| switchBox-package | A package to train and apply K-Top-Scoring-Pair (KTSP)... |
| testingGroup | Testing set phenotypes |
| trainingGroup | Training set phenotypes |
