R/desc-01-AAC.R

In road2stat/protr: Generating Various Numerical Representation Schemes for Protein Sequences

#' Amino Acid Composition Descriptor
#'
#' This function calculates the Amino Acid Composition descriptor (dim: 20).
#'
#' @param x A character vector, as the input protein sequence.
#'
#' @return A length 20 named vector
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{extractDC}} and \code{\link{extractTC}}
#' for Dipeptide Composition and Tripeptide Composition descriptors.
#'
#' @export extractAAC
#'
#' @references
#' M. Bhasin, G. P. S. Raghava.
#' Classification of Nuclear Receptors Based on
#' Amino Acid Composition and Dipeptide Composition.
#' \emph{Journal of Biological Chemistry}, 2004, 279, 23262.
#'
#' @examples
#' x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
#' extractAAC(x)
extractAAC <- function(x) {
  if (protcheck(x) == FALSE) {
    stop("x has unrecognized amino acid type")
  }

  # 20 Amino Acid Abbrevation Dictionary from
  # https://en.wikipedia.org/wiki/Amino_acid#Table_of_standard_amino_acid_abbreviations_and_properties

  AADict <- c(
    "A", "R", "N", "D", "C", "E", "Q", "G", "H", "I",
    "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"
  )

  AAC <- summary(
    factor(strsplit(x, split = "")[[1]], levels = AADict),
    maxsum = 21
  ) / nchar(x)

  AAC
}