compareOrig             function to compare the original matrix of
                        correct classes to each component of the output
                        object for a certain classifier
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                nlcv results on random data with random forest
                        feature selection
nlcvRF_SHS              nlcv results on strong hetero signal data with
                        random forest feature selection
nlcvRF_SS               nlcv results on strong signal data a with
                        random forest feature selection
nlcvRF_WHS              nlcv results on weak signal data with random
                        forest feature selection
nlcvRF_WS               nlcv results on weak hetero signal data with
                        random forest feature selection
nlcvTT_R                nlcv results on random data with t-test feature
                        selection
nlcvTT_SHS              nlcv results on strong hetero signal data with
                        t-test feature selection
nlcvTT_SS               nlcv results on strong signal data a with
                        t-test feature selection
nlcvTT_WHS              nlcv results on weak signal data with t-test
                        feature selection
nlcvTT_WS               nlcv results on weak hetero signal data with
                        t-test feature selection
nldaI                   new MLInterfaces schema for lda from MASS
pamrI                   Instance of a learnerSchema for pamr models
pamrIconverter          convert from 'pamrML' to 'classifierOutput'
pamrML                  Wrapper function around the pamr.* functions
pamrTrain               Function providing a formula interface to
                        pamr.train
predict.pamrML          predict 'pamrML' object
print.nlcvConfusionMatrix
                        print object 'nlcvConfusionMatrix'
print.pamrML            print 'pamrML' object
print.summary.mcrPlot   'print' function for 'summary.mcrPlot' object
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         'summary' function for 'mcrPlot' object
topTable-methods        Methods for topTable
xtable.confusionMatrix
                        xtable method for confusionMatrix objects
xtable.summary.mcrPlot
                        xtable method for summary.mcrPlot objects
