mlDNA: Machine Learning-based Differential Network Analysis of Transcriptome Data

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Functions necessary to perform the machine learning-based differential network analysis of transcriptome data.

Author
Chuang Ma and Xiangfeng Wang
Date of publication
2013-11-19 07:37:01
Maintainer
Chuang Ma <chuangma2006@gmail.com>
License
GPL (>= 2)
Version
1.1
URLs

View on CRAN

Man pages

AverageRankScore
Average-based rank score
classifier
Building machine learning-based classification models
ConditionSpecificGenes
Condition specifically expressed genes
ConvergenceDegree
Calculating covergence degree
cross_validation
Cross validation method
data
example data for mlDNA
exp2net
Inferring transcriptional networks from gene expression data
expFeatureMatrix
Expression-based feature matrix
geneRanker
Gene Ranking
interactionRemoval
interation-removal method
mlDNA-package
Machine Learning-based Differential Network Analysis
netFeatureMatrix
Generating network feature matrix
optimalScore
Identifying optimal prediction score
plotROC
Plotting receiver operating characteristic(ROC) Curves
predictor
Prediction
PSOL_InitialNegativeSelection
Initial negative set selection for building machine...
PSOL_NegativeExpansion
Negative expansion
PSOL_ResultExtraction
PSOL result extraction
randomSeed
Random seed generator

Files in this package

mlDNA
mlDNA/NAMESPACE
mlDNA/data
mlDNA/data/mlDNA.rda
mlDNA/data/datalist
mlDNA/R
mlDNA/R/downstreamAnalysis.R
mlDNA/R/ml.R
mlDNA/R/expression.R
mlDNA/R/net_subfunctions.R
mlDNA/R/PSOL.R
mlDNA/R/net.R
mlDNA/R/Global.R
mlDNA/MD5
mlDNA/DESCRIPTION
mlDNA/man
mlDNA/man/netFeatureMatrix.Rd
mlDNA/man/interactionRemoval.Rd
mlDNA/man/randomSeed.Rd
mlDNA/man/geneRanker.Rd
mlDNA/man/PSOL_ResultExtraction.Rd
mlDNA/man/exp2net.Rd
mlDNA/man/PSOL_InitialNegativeSelection.Rd
mlDNA/man/PSOL_NegativeExpansion.Rd
mlDNA/man/expFeatureMatrix.Rd
mlDNA/man/cross_validation.Rd
mlDNA/man/AverageRankScore.Rd
mlDNA/man/plotROC.Rd
mlDNA/man/ConditionSpecificGenes.Rd
mlDNA/man/classifier.Rd
mlDNA/man/data.Rd
mlDNA/man/optimalScore.Rd
mlDNA/man/ConvergenceDegree.Rd
mlDNA/man/mlDNA-package.Rd
mlDNA/man/predictor.Rd