cisREfindbed            Create and preprocessing of the input for
                        SVM2CRM analysis
createBed               Create bed file of predictions using svm.
createSVMinput          Take the output of findFeatureOverlap and then
                        create a positive and negative set of
                        cis-regulatory elements
featSelectionWithKmeans
                        This function select the most meaningful
                        variables in a matrix of ChIP-seq data using
                        k-means and ICRR.
findFeatureOverlap      Find the overlap of genomic regions between the
                        output of cisREfind and a database of validated
                        cis-regulatory elements.
frequencyHM             frequencyHM
getSignal               Model the signals of each histone marks around
                        genomic features (e.g. enhancers,
                        not_enhancers).
performanceSVM          Estimate the performance of prediction.
plotFscore              Plot the F-score in relation with the
                        sensitivity and specificity
plotROC                 Plot the ROC curve of the best model
predictionGW            Perform prediction of cis-regulatory elements
                        genome-wide
smoothInputFS           Smooth the signals of the histone marks to
                        prepare the input for feature selection
                        analysis
tuningParametersCombROC
                        Test different models using different kernel of
                        SVM, values of cost functions, the number of
                        histone marks.
