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

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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.

Author
Luciano Garofano, Stefano Maria Pagnotta, Michele Ceccarelli
Date of publication
2015-04-20 11:55:18
Maintainer
Luciano Garofano <lucianogarofano88@gmail.com>
License
GPL (>= 3)
Version
1.0
URLs

View on CRAN

Man pages

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

Files in this package

synRNASeqNet
synRNASeqNet/NAMESPACE
synRNASeqNet/R
synRNASeqNet/R/plotPR.R
synRNASeqNet/R/performanceNET.R
synRNASeqNet/R/entropyCS.R
synRNASeqNet/R/Likelihoods.R
synRNASeqNet/R/shrinkageIntensity.R
synRNASeqNet/R/entropyShrink.R
synRNASeqNet/R/entropyBayes.R
synRNASeqNet/R/getTask.R
synRNASeqNet/R/entropyMM.R
synRNASeqNet/R/parMIEstimate.R
synRNASeqNet/R/thetaBayes.R
synRNASeqNet/R/parEntropyEstimate.R
synRNASeqNet/R/simulatedData.R
synRNASeqNet/R/parMIKD.R
synRNASeqNet/R/DiscriminantPower.R
synRNASeqNet/R/diagId.R
synRNASeqNet/R/synRNAseqNet-internal.R
synRNASeqNet/R/YoudenIndex.R
synRNASeqNet/R/performanceIndex.R
synRNASeqNet/R/getIndex.R
synRNASeqNet/R/plotROC.R
synRNASeqNet/R/startId.R
synRNASeqNet/R/entropyML.R
synRNASeqNet/R/beta_k.R
synRNASeqNet/R/aucDisc.R
synRNASeqNet/R/thetaGT.R
synRNASeqNet/R/thetaShrink.R
synRNASeqNet/R/thetaML.R
synRNASeqNet/R/mainNetFunction.R
synRNASeqNet/MD5
synRNASeqNet/DESCRIPTION
synRNASeqNet/man
synRNASeqNet/man/YoudenIndex.Rd
synRNASeqNet/man/performanceIndex.Rd
synRNASeqNet/man/Likelihoods.Rd
synRNASeqNet/man/aucDisc.Rd
synRNASeqNet/man/plotPR.Rd
synRNASeqNet/man/DiscriminantPower.Rd
synRNASeqNet/man/simulatedData.Rd
synRNASeqNet/man/parMIKD.Rd
synRNASeqNet/man/synRNASeqNet-internal.Rd
synRNASeqNet/man/performanceNET.Rd
synRNASeqNet/man/entropyMM.Rd
synRNASeqNet/man/mainNetFunction.Rd
synRNASeqNet/man/plotROC.Rd
synRNASeqNet/man/parMIEstimate.Rd
synRNASeqNet/man/entropyML.Rd
synRNASeqNet/man/entropyCS.Rd
synRNASeqNet/man/parEntropyEstimate.Rd
synRNASeqNet/man/entropyShrink.Rd
synRNASeqNet/man/synRNASeqNet-package.Rd
synRNASeqNet/man/entropyBayes.Rd