R/threshold_precision.R

In fosterlab/PrInCE: Predicting Interactomes from Co-Elution

#' Threshold interactions at a given precision cutoff
#'
#' @param interactions the ranked list of interactions output by
#'   \code{\link[PrInCE]{predict_interactions}}, including a \code{precision}
#'   column
#' @param threshold the minimum precision of the unweighted interaction
#'   network to return
#'
#' @return the subset of the original ranked list at the given precision
#'
#' @examples
#' data(scott)
#' data(scott_gaussians)
#' data(gold_standard)
#' # analyze only the first 100 profiles
#' subset <- scott[seq_len(500), ]
#' gauss <- scott_gaussians[names(scott_gaussians) %in% rownames(subset)]
#' ppi <- PrInCE(subset, gold_standard,
#'   gaussians = gauss, models = 1,
#'   cv_folds = 3
#' )
#' network <- threshold_precision(ppi, threshold = 0.5)
#' nrow(network)
#' @export
threshold_precision <- function(interactions, threshold) {
  upto <- which(interactions$precision >= threshold)
  if (!length(upto)) {
    NULL
  } else {
    interactions[seq_len(max(upto, na.rm = T)), ]
  }
}