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. |