library(devtools)
myGithubUsername <- "AAMargolin"
myGithubPassword <- "Set password here"
install_github("federationPLoSRevision", username="Sage-Bionetworks", auth_user=myGithubUsername, password=myGithubPassword)
require(federationPLoSRevision)
require(BCC)
require(predictiveModeling)
### if not automatically configured
synapseLogin()
metabricTrainingData <- loadMetabricMicmaTrainingData()
coxTestModel <-CoxphModel$new()
coxTestModel$customTrain(metabricTrainingData$exprData, metabricTrainingData$copyData,
metabricTrainingData$clinicalFeaturesData, metabricTrainingData$clinicalSurvData)
modelClassFile <- "/home/ubuntu/SageGit/Sage-Bionetworks/federationPLoSRevision/R/CoxphModel.R"
submitCompetitionModel_micmaTrained(modelName = "CoxTestModel", trainedModel=coxTestModel, rFiles=modelClassFile,
algorithm="boosting", geneList="MASP+clinical")
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