R/desc-08-CTDT.R

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

#' CTD Descriptors - Transition
#'
#' This function calculates the Transition descriptor of the
#' CTD descriptors (dim: 21).
#'
#' @param x A character vector, as the input protein sequence.
#'
#' @return A length 21 named vector
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{extractCTDC}} and \code{\link{extractCTDD}}
#' for Composition and Distribution of the CTD descriptors.
#'
#' @export extractCTDT
#'
#' @note For this descriptor type, users need to intelligently evaluate
#' the underlying details of the descriptors provided, instead of using
#' this function with their data blindly. It would be wise to use some
#' negative and positive control comparisons where relevant to help guide
#' interpretation of the results.
#'
#' @references
#' Inna Dubchak, Ilya Muchink, Stephen R. Holbrook and Sung-Hou Kim.
#' Prediction of protein folding class using global description of
#' amino acid sequence. \emph{Proceedings of the National Academy of Sciences}.
#' USA, 1995, 92, 8700-8704.
#'
#' Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou Kim.
#' Recognition of a Protein Fold in the Context of the SCOP classification.
#' \emph{Proteins: Structure, Function and Genetics}, 1999, 35, 401-407.
#'
#' @examples
#' x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
#' extractCTDT(x)
extractCTDT <- function(x) {
  if (protcheck(x) == FALSE) {
    stop("x has unrecognized amino acid type")
  }

  group1 <- list(
    "hydrophobicity" = c("R", "K", "E", "D", "Q", "N"),
    "normwaalsvolume" = c("G", "A", "S", "T", "P", "D", "C"),
    "polarity" = c("L", "I", "F", "W", "C", "M", "V", "Y"),
    "polarizability" = c("G", "A", "S", "D", "T"),
    "charge" = c("K", "R"),
    "secondarystruct" = c("E", "A", "L", "M", "Q", "K", "R", "H"),
    "solventaccess" = c("A", "L", "F", "C", "G", "I", "V", "W")
  )

  group2 <- list(
    "hydrophobicity" = c("G", "A", "S", "T", "P", "H", "Y"),
    "normwaalsvolume" = c("N", "V", "E", "Q", "I", "L"),
    "polarity" = c("P", "A", "T", "G", "S"),
    "polarizability" = c("C", "P", "N", "V", "E", "Q", "I", "L"),
    "charge" = c(
      "A", "N", "C", "Q", "G", "H", "I", "L",
      "M", "F", "P", "S", "T", "W", "Y", "V"
    ),
    "secondarystruct" = c("V", "I", "Y", "C", "W", "F", "T"),
    "solventaccess" = c("R", "K", "Q", "E", "N", "D")
  )

  group3 <- list(
    "hydrophobicity" = c("C", "L", "V", "I", "M", "F", "W"),
    "normwaalsvolume" = c("M", "H", "K", "F", "R", "Y", "W"),
    "polarity" = c("H", "Q", "R", "K", "N", "E", "D"),
    "polarizability" = c("K", "M", "H", "F", "R", "Y", "W"),
    "charge" = c("D", "E"),
    "secondarystruct" = c("G", "N", "P", "S", "D"),
    "solventaccess" = c("M", "S", "P", "T", "H", "Y")
  )

  xSplitted <- strsplit(x, split = "")[[1]]
  n <- nchar(x)

  G <- vector("list", 7)
  for (i in 1:7) G[[i]] <- rep(NA, n)

  # Get groups for each property & each amino acid

  for (i in 1:7) {
    try(G[[i]][which(xSplitted %in% group1[[i]])] <- "G1")
    try(G[[i]][which(xSplitted %in% group2[[i]])] <- "G2")
    try(G[[i]][which(xSplitted %in% group3[[i]])] <- "G3")
  }

  # Combine single amino acids by a 2-length step

  for (i in 1:7) G[[i]] <- paste(G[[i]][-n], G[[i]][-1], sep = "")
  G <- lapply(G, function(x)
    factor(x, levels = c(
      "G1G2", "G2G1", "G1G3",
      "G3G1", "G2G3", "G3G2",
      "G1G1", "G2G2", "G3G3"
    )))

  GSummary <- lapply(G, summary)

  # Compute (n_rs + n_sr) / (N - 1)

  CTDT <- vector("list", 7)

  for (i in 1:7) {
    CTDT[[i]][1] <- sum(GSummary[[i]][c("G1G2", "G2G1")]) / (n - 1)
    CTDT[[i]][2] <- sum(GSummary[[i]][c("G1G3", "G3G1")]) / (n - 1)
    CTDT[[i]][3] <- sum(GSummary[[i]][c("G2G3", "G3G2")]) / (n - 1)
  }

  CTDT <- unlist(CTDT)

  names(CTDT) <- paste(
    "prop", rep(1:7, each = 3), ".",
    rep(c("Tr1221", "Tr1331", "Tr2332"), times = 7),
    sep = ""
  )

  CTDT
}