mAPKL (version 1.4.2)

netwAttr: Calculates network characteristics

Description

Calculate some basic network characteristics of the top ranked genes

Usage

netwAttr(mAPKLObj, net="clr")

Arguments

mAPKLObj

An object of mAPKL class.

net

The network reconstruction method to be employed. The user may select between "clr" (default), "aracne.a" and "aracne.m".

Value

• Upon successful completion, the function returns an NetAttr object.

Details

It calculates some basic network characteristics. Those include the "degree", the "closeness", the "betweenness", and finally the "transitivity" or else clustering coefficient. We calculate the weighted values for both local and global scores. The three available network reconstruction options are: clr: Context Likelihood or Relatedness Network aracne.a: Algorithm for the Reconstruction of Accurate Cellular Networks (additive model) aracne.m: Algorithm for the Reconstruction of Accurate Cellular Networks (multiplicative model)

Examples

library(mAPKLData)
data(mAPKLData)
breast <- sampling(Data=mAPKLData, valPercent=40, classLabels="type", seed=135)
normTrainData <- preprocess(breast$trainData)
normTestData <- preprocess(breast$testData)

exprs(breast$trainData) <- normTrainData$clL2.normdata
exprs(breast$testData) <- normTestData$clL2.normdata

out.clL2 <- mAPKL(trObj=breast$trainData, classLabels="type",
valObj=breast$testData, dataType=7)

net.attr <- netwAttr(mAPKLObj=out.clL2)