netClass: netClass: An R Package for Network-Based Biomarker Discovery

Share:

netClass is an R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. This package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: 1) average gene expression of pathway (aep); 2) pathway activities classification (PAC); 3) Hub network Classification (hubc); 4) filter via top ranked genes (FrSVM); 5) network smoothed t-statistic (stSVM).

Author
Yupeng Cun
Date of publication
2013-12-03 22:44:46
Maintainer
Yupeng Cun <yupeng.cun@gmail.com>
License
GPL (>= 2)
Version
1.2.1

View on CRAN

Man pages

ad.matrix
An adjacency matrix of a sample graph...
calc.diffusionKernelp
Computing the Random Walk Kernel matrix of network
classify.aep
Training and predicting using aepSVM (aepSVM) classification...
classify.frsvm
Training and predicting using FrSVM
classify.hubc
Training and predicting using hub nodes classification...
classify.pac
Training and predicting using PAC classification methods
classify.stsvm
Training and predicting using stSVM classification methods
cv.aep
Cross validation for aepSVM (aepSVM)
cv.frsvm
Cross validation for FrSVM
cv.hubc
Cross validation for hub nodes classification
cv.pac
Cross validation for Pathway Activities Classification(PAC)
cv.stsvm
Cross validation for smoothed t-statistic to select...
EN2SY
An list for mapping gene entre ids to symbol ids
expr
Two expression profile matrixs and their labels
getGeneRanking
Get gene ranking based on geneRank algorithm.
getGraphRank
Random walk kernel matrix smoothing t-statistic
Gs2
An subgraph of hub nodes
netClass-package
An R package for network-Based microarray Classification
pGeneRANK
GeneRANK
pOfHubs
Computing p value of hubs using the permutation test
predictAep
Predicting the test tdata using aep trained model
predictFrsvm
Predicting the test data using frsvm trained model
predictHubc
Predicting the test data using hubc trained model
predictPac
Predicting the test data using pac trained model
predictStsvm
Predicting the test data using stsvm trained model
probeset2pathway
Generae a mean gene expression of genes of each pathway...
probeset2pathwayTrain
Search CROG in training data
probeset2pathwayTst
Applied CROG to testing data
train.aep
Training the data using aep methods
train.frsvm
Training the data using frsvm method
train.hubc
Predicting the data using hub nodes classification model
train.pac
Training the data using pac methods
train.stsvm
Training the data using stsvm methods

Files in this package

netClass
netClass/NAMESPACE
netClass/data
netClass/data/expr.rda
netClass/data/EN2SY.rda
netClass/data/Gs2.rda
netClass/data/datalist
netClass/data/ad.matrix.rda
netClass/R
netClass/R/hubNetworkAnalysisCV.R
netClass/R/pacCV.R
netClass/R/FrSVM.R
netClass/R/averageExpressionPathwaySVM.R
netClass/R/stSVM.R
netClass/vignettes
netClass/vignettes/Vignettes.pdf
netClass/MD5
netClass/DESCRIPTION
netClass/man
netClass/man/predictPac.Rd
netClass/man/predictHubc.Rd
netClass/man/cv.frsvm.Rd
netClass/man/train.stsvm.Rd
netClass/man/classify.aep.Rd
netClass/man/predictFrsvm.Rd
netClass/man/train.pac.Rd
netClass/man/cv.aep.Rd
netClass/man/predictStsvm.Rd
netClass/man/calc.diffusionKernelp.Rd
netClass/man/EN2SY.Rd
netClass/man/expr.Rd
netClass/man/getGeneRanking.Rd
netClass/man/train.hubc.Rd
netClass/man/train.frsvm.Rd
netClass/man/classify.frsvm.Rd
netClass/man/classify.hubc.Rd
netClass/man/pOfHubs.Rd
netClass/man/probeset2pathwayTrain.Rd
netClass/man/classify.stsvm.Rd
netClass/man/classify.pac.Rd
netClass/man/cv.hubc.Rd
netClass/man/ad.matrix.Rd
netClass/man/train.aep.Rd
netClass/man/probeset2pathway.Rd
netClass/man/probeset2pathwayTst.Rd
netClass/man/getGraphRank.Rd
netClass/man/pGeneRANK.Rd
netClass/man/cv.pac.Rd
netClass/man/predictAep.Rd
netClass/man/cv.stsvm.Rd
netClass/man/Gs2.Rd
netClass/man/netClass-package.Rd