Package DRWPClassGM implements the DRW-GM method. DRW-GM is a pathway-based classification method which performs classifier construction and precise disease status prediction by joint analysis of genomic and metabolomic data and pathway topology. How to use DRWPClassGM Essential dependence platform To run DRWPClassGM, you should make sure that your computer has installed Weka. The Weka downloaded website (in our analysis we installed weka-3-7-12jre.exe): http://www.cs.waikato.ac.nz/~ml/weka/downloading.html
The available resource of DRWPClass can be downloaded as follows: Package source: DRWPClassGM_1.0.tar.gz
Windows binary: DRWPClassGM_1.0.zip
Reference manual: DRWPClassGM-manual.pdf
http://222.170.78.208/DRW-GM/
Dependent packages: Depends: R (>= 3.1.1), igraph, Matrix, RWeka, samr
library(DRWPClassGM)
data(GProf8511) data(GProf3325) data(MProf) data(pathSet) data(dGMGraph)
fit <- fit.DRWPClassGM(xG=GProf8511$mRNA_matrix, yG.class1=GProf8511$normal, yG.class2=GProf8511$PCA, xM=MProf$Meta_matrix, yM.class1=MProf$normal, yM.class2=MProf$PCA, DEBUG=TRUE, pathSet=pathSet, globalGraph=dGMGraph, testStatistic="t-test", classifier = "Logistic")
predict.DRWPClassGM(object=fit, newx=GProf3325$mRNA_matrix[,c(GProf3325$normal,GProf3325$PCA)], type = "class")
evaluate.DRWPClassGM(object=fit, newx=GProf3325$mRNA_matrix, newy.class1=GProf3325$normal, newy.class2=GProf3325$PCA)
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