R/get_aa_transition_matrix.R

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

#' Get an amino acid transition matrix
#'
#' From Dang, Cuong Cao, et al. "FLU, an amino acid substitution model for
#' influenza proteins." BMC evolutionary biology 10.1 (2010): 99.
#'
#' File downloaded from \code{
#'   ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU/Flu_All_it2.txt_PAML.txt
#' }
#'
#' As can be seen in \url{
#'   https://github.com/stephaneguindon/phyml/blob/master/src/io.c#L3188
#' }, the column names are \code{Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu
#' Lys Met Phe Pro Ser Thr Trp Tyr Val}
#' @inheritParams default_params_doc
#' @return a tibble, with column names equal to the uppercase
#'   amino acid name
#' @author Richèl J.C. Bilderbeek
#' @export
get_aa_transition_matrix <- function(
  transition_matrix_name
) {
  if (transition_matrix_name == "BLOSUM62") {
    BLOSUM62 <- NULL; rm(BLOSUM62) # nolint, fixes warning: no visible binding for global variable
    utils::data("BLOSUM62", package = "Biostrings")
    return(BLOSUM62)
  } else if (transition_matrix_name == "BLOSUM80") {
    BLOSUM80 <- NULL; rm(BLOSUM80) # nolint, fixes warning: no visible binding for global variable
    utils::data("BLOSUM80", package = "Biostrings")
    return(BLOSUM80)
  } else if (transition_matrix_name == "FLU") {
    t <- as.matrix(
      readr::read_csv(
        system.file("extdata", "flu_transitions.csv", package = "bbbq"),
        col_types = readr::cols(.default = readr::col_double())
      )
    )
    rownames(t) <- colnames(t)
    return(t)
  } else {
    stop(
      "Unknown 'transition_matrix_name' with value '",
      transition_matrix_name, "'. \n",
      "Tip: use BLOSUM62, BLOSUM80 or FLU"
    )
  }
}