R/generate_amr_taxonomy.R

In epi2me2r: Process Nanopore EPI2ME Output for Use in R

#' Generates a taxonomy file for AMR count table
#' @name generate_amr_taxonomy
#' @param amr.count.table count of AMR genes with CVTERMID in the
#' first row and samples on columns
#' @param verbose TRUE or FALSE: whether to keep all columns of AMR gene
#' information or not. Default FALSE.
#' @return data table of taxonomy of AMR genes in count table
#' @examples
#' \dontrun{
#' generate_amr_taxonomy(amr.count.table = amr.count.table, verbose = FALSE)
#' }
#' @import data.table
#' @export

data(CARD_taxonomy, envir=environment())

generate_amr_taxonomy <- function(amr.count.table, verbose=FALSE){
  amr.CVTERMID.list <- amr.count.table[, 1]
  amr.CVTERMID.list$CVTERMID <- as.numeric(amr.CVTERMID.list$CVTERMID)
  CARD_taxonomy$CVTERMID <- as.numeric(CARD_taxonomy$CVTERMID)
  merged.data <- merge(x = amr.CVTERMID.list, y = CARD_taxonomy,
                       by = "CVTERMID", all.x = TRUE)
  if (verbose) {
    taxa_long <- merged.data[, c("CVTERMID", "ARO Accession",
                                 "CARDversion", "Model Sequence ID", "Model ID",
                                 "Model Name", "ARO Name", "Protein Accession",
                                 "DNA Accession",
                                 "AMR Gene Family", "Drug Class",
                                 "Resistance Mechanism", "mutationassociated")]
    taxa_long
  } else {
    taxa_short <- merged.data[, c("CVTERMID","Drug Class", "AMR Gene Family",
                                  "Resistance Mechanism", "ARO Name")]
    taxa_short
  }
}