#' Load training data for the metabric reevaluation
#'
#' Loads data for gene expression, copy number, clinical covariates and clinical survival times for the training dataset
#' used to train predicitve models.
#'
#' @return a list with elements: exprData, containing an ExpressionSet of gene expression features;
#' copyData, containing an ExpressionSet of copy number features; clinicalFeaturesData, containing an
#' AnnotatedDataFrame of clinical covariates; and clinicalSurvData, containing a Surv object
#' of survival times and censor values.
#' @author Adam Margolin and In Sock
#' @export
loadFederationMetabricTrainingData <- function(){
metabricTrainingData <- list()
idExpressionLayer <- "syn1588845"
expressionLayer <- loadEntity(idExpressionLayer)
metabricTrainingData$exprData <- expressionLayer$objects[[1]]
idCopyLayer <- "syn1589116"
copyLayer <- loadEntity(idCopyLayer)
metabricTrainingData$copyData <- copyLayer$objects[[1]]
idClinicalFeaturesLayer <- "syn1670337"
clinicalFeaturesLayer <- loadEntity(idClinicalFeaturesLayer)
metabricTrainingData$clinicalFeaturesData <- clinicalFeaturesLayer$objects$TraingData1CFData
idClinicalSurvLayer <- "syn1643540"
clinicalSurvLayer <- loadEntity(idClinicalSurvLayer)
metabricTrainingData$clinicalSurvData <- clinicalSurvLayer$objects$clinicalSurv_train
return(metabricTrainingData)
}
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