R/misc-04-protseg.R

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

#' Protein Sequence Segmentation/Partition
#'
#' This function extracts the segmentations from the protein sequence.
#'
#' @param x A character vector, as the input protein sequence.
#'
#' @param aa A character, the amino acid type. One of
#' \code{'A'}, \code{'R'}, \code{'N'}, \code{'D'},
#' \code{'C'}, \code{'E'}, \code{'Q'}, \code{'G'},
#' \code{'H'}, \code{'I'}, \code{'L'}, \code{'K'},
#' \code{'M'}, \code{'F'}, \code{'P'}, \code{'S'},
#' \code{'T'}, \code{'W'}, \code{'Y'}, \code{'V'}.
#'
#' @param k A positive integer, specifys the window size
#' (half of the window), default is 7.
#'
#' @return A named list, each component contains one of the
#' segmentations (a character string), names of the list components
#' are the positions of the specified amino acid in the sequence.
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export protseg
#'
#' @examples
#' x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
#' protseg(x, aa = "R", k = 5)
protseg <- function(
  x, aa = c(
    "A", "R", "N", "D", "C",
    "E", "Q", "G", "H", "I",
    "L", "K", "M", "F", "P",
    "S", "T", "W", "Y", "V"
  ), k = 7) {
  aa <- match.arg(aa)

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

  CenterIdx <- which(xSplitted == aa)

  if (length(CenterIdx) < 0.5) {
    stop(paste("Did not find AA", aa, "in the sequence"))
  }

  CenterIdx <- CenterIdx[(CenterIdx - k) > 0.5 & (CenterIdx + k) < (n + 0.5)]

  if (length(CenterIdx) < 0.5) {
    stop(paste("Segmentation does not exist for amino acid", aa, "and step", k))
  }

  segments <- vector("list", length(CenterIdx))

  for (i in 1:length(CenterIdx)) {
    segments[[i]] <- paste(
      xSplitted[(CenterIdx[i] - k):(CenterIdx[i] + k)],
      collapse = ""
    )
  }

  names(segments) <- as.character(CenterIdx)

  segments
}