R/filter_best_hits.R

In drostlab/rdiamond: Seamless Integration of DIAMOND2 Sequence Searches in R

#' @title Helper function to select best DIAMOND hit based on minimum evalue
#' @details Extracts the best hit based on lowest e-value and longest splice variant
#' when e-values are equal
#' @param x a tibble storing gene locus ids, splice variant ids, and blast output for filtering
#' @author Hajk-Georg Drost
#'
filter_best_hits <- function(x) {
  
  if (nrow(x) == 0)
    stop("When trying to retrieve the best hit the column ",x," was empty and could not be processed. Please remove this line from the dataset, before extracting best hits.", call. = FALSE)
  min_val <- min(x$evalue)
  evalue <- alig_length <- NULL
  res <- dplyr::filter(x, evalue == min_val)
  if (nrow(res) > 1) {
    max_len <- max(res$alig_length)
    res <- dplyr::filter(res, alig_length == max_len)
  }
  
  if (nrow(res) > 1)
    res <- dplyr::slice(res, 1)
  
  return(res)
}