| classify | Wrapper to run all classifiers for one run |
| confusionMatrix.nlcv | compute a confusion matrix for the optimal number of features for a given technique used in the nested loop cross validation |
| inTrainingSample | Function to define a learning sample based on balanced sampling |
| limmaTwoGroups | Wrapper around limma for the comparison of two groups |
| mcrPlot | Misclassification Rate Plot |
| nlcv | Nested Loop Cross-Validation |
| nlcvRF_R | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvRF_SHS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvRF_SS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvRF_WHS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvRF_WS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvTT_R | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvTT_SHS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvTT_SS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvTT_WHS | Simulated Datasets to Demonstrate nlcv Functionality |
| nlcvTT_WS | Simulated Datasets to Demonstrate nlcv Functionality |
| nldaI | new MLInterfaces schema for lda from MASS |
| pamrI | Instance of a learnerSchema for pamr models |
| pamrML | Wrapper function around the pamr.* functions |
| pamrTrain | Function providing a formula interface to pamr.train |
| predict.pamrML | Wrapper function around the pamr.* functions |
| print.nlcvConfusionMatrix | compute a confusion matrix for the optimal number of features for a given technique used in the nested loop cross validation |
| print.pamrML | Wrapper function around the pamr.* functions |
| print.summary.mcrPlot | Misclassification Rate Plot |
| rankDistributionPlot | Plot the Distribution of Ranks of Features Across nlcv Runs |
| rocPlot | Produce a ROC plot for a classification model belonging to a given technique and with a given number of features. |
| scoresPlot | Function to Plot a Scores Plot |
| summary.mcrPlot | Misclassification Rate Plot |
| topTable | Methods for topTable |
| topTable-method | Methods for topTable |
| topTable-methods | Methods for topTable |
| xtable.confusionMatrix | xtable method for confusionMatrix objects |
| xtable.summary.mcrPlot | xtable method for summary.mcrPlot objects |