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SVM2CRM (version 1.4.0)

SVM2CRM: support vector machine for cis-regulatory elements detections

Description

Detection of cis-regulatory elements using svm implemented in LiblineaR.

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Version

Version

1.4.0

License

GPL-3

Maintainer

Guidantonio Malagoli Tagliazucchi

Last Published

February 15th, 2017

Functions in SVM2CRM (1.4.0)

cisREfindbed

Create and preprocessing of the input for SVM2CRM analysis
getSignal

Model the signals of each histone marks around genomic features (e.g. enhancers, not_enhancers).
perfomanceSVM

Estimate the performance of prediction.
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
plotFscore

Plot the F-score in relation with the sensitivity and specificity
frequencyHM

frequencyHM
plotROC

Plot the ROC curve of the best model
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.
predictionGW

Perform prediction of cis-regulatory elements genome-wide
tuningParametersCombROC

Test different models using different kernel of SVM, values of cost functions, the number of histone marks.
smoothInputFS

Smooth the signals of the histone marks to prepare the input for feature selection analysis