synRNASeqNet (version 1.0)

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

Description

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.

Index

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