mlDNA: Machine Learning-based Differential Network Analysis of Transcriptome Data
Version 1.1

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

Browse man pages Browse package API and functions Browse package files

AuthorChuang Ma and Xiangfeng Wang
Date of publication2013-11-19 07:37:01
MaintainerChuang Ma <chuangma2006@gmail.com>
LicenseGPL (>= 2)
Version1.1
URL http://www.cmbb.arizona.edu/mlDNA
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mlDNA")

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

Functions

AverageRankScore Man page Source code
ConditionSpecificGenes Man page Source code
ConvergenceDegree Man page Source code
DNA.ConnectivityNum Source code
DNA.NIndex2knodes Source code
DNA.closeness Source code
DNA.connectivitylist Source code
DNA.distance Source code
DNA.distance2knowngenes Source code
DNA.eccentricity Source code
DNA.getNodeProperty Source code
EDist Source code
PSOL_InitialNegativeSelection Man page Source code
PSOL_NegativeExpansion Man page Source code
PSOL_ResultExtraction Man page Source code
checkDistmat Source code
checkExpMat Source code
checkadjmatrix Source code
classifier Man page Source code
cor.threshold Source code
cross_validation Man page Source code
cv Source code
cvSampleIndex Source code
data Man page
difExp Source code
exp2net Man page Source code
expFeatureMatrix Man page Source code
expFun Source code
expMean Source code
filterLowCorrelation Source code
find_ClassifierWithMaxAUC Source code
formatAdj2Graph Source code
geneRanker Man page Source code
getIndex Source code
getNodeProperty Source code
getsgene Source code
interactionRemoval Man page Source code
matZScore Source code
mlDNA Man page
mlDNA-package Man page
netFeatureMatrix Man page Source code
network.differences Source code
network.properties Source code
obtain_CV_AUCMat Source code
one_cross_validation Source code
optimalScore Man page Source code
permutMatrix Source code
permutThreshold Source code
plotLines Source code
plotROC Man page Source code
predictor Man page Source code
randomSeed Man page Source code
saltData Man page
uniqueTissues Source code

Files

NAMESPACE
data
data/mlDNA.rda
data/datalist
R
R/downstreamAnalysis.R
R/ml.R
R/expression.R
R/net_subfunctions.R
R/PSOL.R
R/net.R
R/Global.R
MD5
DESCRIPTION
man
man/netFeatureMatrix.Rd
man/interactionRemoval.Rd
man/randomSeed.Rd
man/geneRanker.Rd
man/PSOL_ResultExtraction.Rd
man/exp2net.Rd
man/PSOL_InitialNegativeSelection.Rd
man/PSOL_NegativeExpansion.Rd
man/expFeatureMatrix.Rd
man/cross_validation.Rd
man/AverageRankScore.Rd
man/plotROC.Rd
man/ConditionSpecificGenes.Rd
man/classifier.Rd
man/data.Rd
man/optimalScore.Rd
man/ConvergenceDegree.Rd
man/mlDNA-package.Rd
man/predictor.Rd
mlDNA documentation built on May 20, 2017, 3:14 a.m.