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netClass (version 1.0)

netClass: An R Package for Network-Based Microarray Classification

Description

netClass is an R packages for feature (gene) selection, which employ the biological network information to microarray classification. We implemented average gene expression of pathway (aep), pathway activities classification (PAC), Hub network Classification, filter via top ranked genes(FrSVM), smoothed t-statistic(stSVM) for two classes microarray classification which employed the prior information.

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Version

Install

install.packages('netClass')

Monthly Downloads

12

Version

1.0

License

GPL (>= 2)

Maintainer

Yupeng Cun

Last Published

May 30th, 2013

Functions in netClass (1.0)

calc.diffusionKernelp

Computing the Random Walk Kernel matrix of network
getGeneRanking

Get gene ranking based on geneRank algorithm.
expr

Two expression profile matrixs and their labels
classify.frsvm

Training and predicting using FrSVM
classify.stsvm

Training and predicting using stSVM classification methods
Gs2

An subgraph of hub nodes
getGraphRank

Random walk kernel matrix smoothing t-statistic
classify.hubc

Training and predicting using hub nodes classification methods
classify.aep

Training and predicting using aepSVM (aepSVM) classification methods
probeset2pathway

Generae a mean gene expression of genes of each pathway matrix
classify.pac

Training and predicting using PAC classification methods
probeset2pathwayTst

Applied CROG to testing data
stsvm.cv

Cross validation for smoothed t-statistic to select significant top ranked differential expressed genes
hubc.cv

Cross validation for hub nodes classification
pac.cv

Cross validation for Pathway Activities Classification(PAC)
ad.matrix

An adjacency matrix of a sample graph...
aep.cv

Cross validation for aepSVM (aepSVM)
pGeneRANK

GeneRANK
netClass-package

An R package for network-Based microarray Classification
FrSVM.cv

Cross validation for FrSVM
probeset2pathwayTrain

Search CROG in training data
pOfHubs

Computing p value of hubs using the permutation test