R/rf_classPredict.R

In pcahan1/cancerCellNet: CellNet, for cancer

#' @title
#' Classify Query Samples
#'
#' @description
#' Classify the transformed query data using the random forest classifier.
#'
#' @param rfObj random forest object created from \code{\link{makeClassifier}}
#' @param expQuery transformed query data created from \code{\link{query_transform}}
#' @param numRand number of random profiles to add into the classification
#'
#' @return a classification matrix of the query data
#' @export
rf_classPredict<-function(rfObj, expQuery, numRand=50) {

  randDat = randomize(expQuery, num=numRand) # generate the random profiles
  expQuery = cbind(expQuery, randDat)

  preds = rownames(rfObj$importance)
  xpreds = t(predict(rfObj, t(expQuery[preds,]), type='prob'))
  colnames(xpreds) = colnames(expQuery)

  return(xpreds)
}