synRNASeqNet-package: Synthetic RNA-Seq Network Generation and Mutual Information...

Description Index Author(s)


It implements various estimators of mutual information, such as the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, the shrinkage estimator, and the Chao-Shen estimator. It also offers wrappers to the kNN and kernel density estimators.

Furthermore, it provides various index of performance evaluation such as precision, recall, FPR, F-Score, ROC-PR Curves and so on.

Lastly, it provides a brand new way of generating synthetic RNA-Seq Network with known dependence structure.


synRNASeqNet-package: Synthetic RNA-Seq Network Generation and Mutual Information Estimates
parMIEstimate: Parallel Mutual Information Estimation
parEntropyEstimate: Parallel Entropy Estimation
entropyML: Maximum Likelihood Entropy Estimate
entropyMM: Miller-Madow corrected Entropy Estimate
entropyBayes: Bayesian Entropy Estimate
entropyCS: Chao-Shen Entropy Estimate
entropyShrink: James-Stein Shrinkage Entropy Estimate
parMIKD: Parallel Kernel Density Mutual Information Estimate
simulatedData: Random Generation Networks for RNA-Seq Data
mainNetFunction: Main Estimation and Evaluation Function
plotROC: Plot ROC Curve
plotPR: Plot PR Curve
aucDisc: Calculate Area Under a (ROC/PR) Curve
performanceIndex: Evalutate Performance Indices
performanceNET: Evalutate Performance Indices
YoudenIndex: Youden's Index
Likelihoods: Likelihood Indices
DiscriminantPower: Discriminant Power


Luciano Garofano [email protected], Stefano Maria Pagnotta, Michele Ceccarelli

lucgar/synRNASeqNet documentation built on May 21, 2017, 3:39 p.m.