#' createFeatureAndResponseDataList
#'
#' Prepares data for input to predictive modeling by matching column names of feature and response data and creating
#' feature and response matrices with columns in the same order
#'
#' @param featureData a matrix of feature data with samples on rows and features on columns
#' @param responseData a matrix or AnnotatedDataFrame of pheno data with samples on rows and features on columns
#' @return a list containing two items: the feature data and the response data with intersecting sample names
#'
#' @author Adam Margolin
#' @export
createFeatureAndResponseDataList <- function(featureData, responseData){
if(is(responseData, "AnnotatedDataFrame")) {
responseData <- pData(responseData)
}
if (is.data.frame(responseData) || is.matrix(responseData)){
commonRowNames <- intersect(rownames(featureData), rownames(responseData))
featureAndResponseDataList <- list(featureData = featureData[commonRowNames,], responseData = responseData[commonRowNames,])
}else if (is.numeric(responseData)){
commonRowNames <- intersect(rownames(featureData), names(responseData))
featureAndResponseDataList <- list(featureData = featureData[commonRowNames,], responseData = responseData[commonRowNames])
}else{
print("error: uknown responseData type")
}
return(featureAndResponseDataList)
}
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