synRNASeqNet: Synthetic RNA-Seq Network Generation and Mutual Information Estimates
Version 1.0

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.

AuthorLuciano Garofano, Stefano Maria Pagnotta, Michele Ceccarelli
Date of publication2015-04-20 11:55:18
MaintainerLuciano Garofano <lucianogarofano88@gmail.com>
LicenseGPL (>= 3)
Version1.0
URL https://github.com/lucgar/synRNASeqNet
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("synRNASeqNet")

Getting started

Package overview

Popular man pages

DiscriminantPower: Discriminant Power
entropyCS: Chao-Shen Entropy Estimate
entropyMM: Miller-Madow corrected Entropy Estimate
parMIEstimate: Parallel Mutual Information Estimation
performanceIndex: Evalutate Performance Indices
plotROC: Plot ROC Curve
synRNASeqNet-package: Synthetic RNA-Seq Network Generation and Mutual Information...
See all...

All man pages Function index File listing

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

Functions

DiscriminantPower Man page Source code
Likelihoods Man page Source code
YoudenIndex Man page Source code
aucDisc Man page Source code
beta_k Man page Source code
diagId Man page Source code
entropyBayes Man page Source code
entropyCS Man page Source code
entropyML Man page Source code
entropyMM Man page Source code
entropyShrink Man page Source code
getIndex Man page Source code
getTask Man page Source code
mainNetFunction Man page Source code
parEntropyEstimate Man page Source code
parMIEstimate Man page Source code
parMIKD Man page Source code
performanceIndex Man page Source code
performanceNET Man page Source code
plotPR Man page Source code
plotROC Man page Source code
shrinkageIntensity Man page Source code
simulatedData Man page Source code
startId Man page Source code
synRNASeqNet Man page
synRNASeqNet-package Man page
thetaBayes Man page Source code
thetaGT Man page Source code
thetaML Man page Source code
thetaShrink Man page Source code

Files

NAMESPACE
R
R/plotPR.R
R/performanceNET.R
R/entropyCS.R
R/Likelihoods.R
R/shrinkageIntensity.R
R/entropyShrink.R
R/entropyBayes.R
R/getTask.R
R/entropyMM.R
R/parMIEstimate.R
R/thetaBayes.R
R/parEntropyEstimate.R
R/simulatedData.R
R/parMIKD.R
R/DiscriminantPower.R
R/diagId.R
R/synRNAseqNet-internal.R
R/YoudenIndex.R
R/performanceIndex.R
R/getIndex.R
R/plotROC.R
R/startId.R
R/entropyML.R
R/beta_k.R
R/aucDisc.R
R/thetaGT.R
R/thetaShrink.R
R/thetaML.R
R/mainNetFunction.R
MD5
DESCRIPTION
man
man/YoudenIndex.Rd
man/performanceIndex.Rd
man/Likelihoods.Rd
man/aucDisc.Rd
man/plotPR.Rd
man/DiscriminantPower.Rd
man/simulatedData.Rd
man/parMIKD.Rd
man/synRNASeqNet-internal.Rd
man/performanceNET.Rd
man/entropyMM.Rd
man/mainNetFunction.Rd
man/plotROC.Rd
man/parMIEstimate.Rd
man/entropyML.Rd
man/entropyCS.Rd
man/parEntropyEstimate.Rd
man/entropyShrink.Rd
man/synRNASeqNet-package.Rd
man/entropyBayes.Rd
synRNASeqNet documentation built on May 19, 2017, 5:10 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.