R/calculateTC_Sm.R

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

    #' calculateTC_Sm
    #' @title Calculate Tripeptide Composition (TC) Descriptor from Biochemical
    #' Similarity Classes
    #' @param x A data.frame containing gene/protein names and their fasta
    #' sequences.
    #' @return A length 216  named vector for the data input.
    #' @seealso See \code{\link{calculateTC}} for Tripeptide Composition
    #' descriptor.
    #' @author Matineh Rahmatbakhsh, \email{matinerb.94@gmail.com}
    #' @importFrom magrittr set_rownames
    #' @description This function calculates Tripeptide Composition (TC)
    #' descriptor from biochemical similarity classes.
    #' @export
    #' @references
    #' Ahmed, I., Witbooi, P., and Christoffels, A. (2018). Prediction of
    #' human-Bacillus anthracis protein–protein interactions using multi-layer
    #' neural network.\emph{Bioinformatics} 34, 4159–4164.
    #'
    #' Cui, G., Fang, C., and Han, K. (2012). Prediction of protein-protein
    #' interactions between viruses and human by an SVM model.
    #' \emph{BMC bioinformatics}, 1–10.
    #'
    #' @examples
    #' data(UP000464024_df)
    #' x_df <- calculateTC_Sm(UP000464024_df)
    #' head(x_df, n = 2L)
    calculateTC_Sm <- function(x) {
      if (!is.data.frame(x)) x <- is.data.frame(x)

      . <- NULL
      V1 <- NULL

      # convert data frame to list
      fastalist <-
        as.list(unlist(x[, 2]))
      names(fastalist) <-
        unlist(x[, 1])

      # check if there is any unrecognized amino acid
      f <- .checkFASTA(fastalist)
      if (nrow(f) > 0) {
        stop("Fastalist has unrecognized amino acid type")
      }

      classes <- vector("list", 6)
      classes[[1]] <- c("I", "V", "L", "M")
      classes[[2]] <- c("F", "Y", "W")
      classes[[3]] <- c("H", "K", "R")
      classes[[4]] <- c("D", "E")
      classes[[5]] <- c("Q", "N", "T", "P")
      classes[[6]] <- c("A", "C", "G", "S")


      vspace <- expand.grid(seq_len(6), seq_len(6), seq_len(6))

      BSlict <- vector("list", 216)

      for (i in seq_len(216)) {
        tmp <- as.vector(outer(classes[[vspace[i, 1]]],
          classes[[vspace[i, 2]]], paste,
          sep = ""
        ))
        BSlict[[i]] <- as.vector(outer(tmp,
          classes[[vspace[i, 3]]], paste,
          sep = ""
        ))
      }
      names(BSlict) <- paste(seq_len(length(BSlict)))



      # compute TC_Sm
      p <- function(x, BSlict) {
        f <-
          x %>%
          lapply(., function(x) strsplit(x[[1]], "")) %>%
          lapply(., function(x) {
            paste(paste(x[[1]][-c(length(x[[1]]), length(x[[1]]) - 1)],
              x[[1]][-c(1, length(x[[1]]))],
              sep = ""
            ), x[[1]][-c(1, 2)],
            sep = ""
            )
          })

        inter <- unlist(lapply(BSlict, function(X) {
          lapply(f, function(Y) {
            length(which(Y %in% X))
          })
        }), recursive = FALSE)

        s <-
          do.call(cbind, inter) %>%
          set_rownames(names(x))
        s <- t(apply(s, 1, function(x) (x - min(x)) / (max(x) - min(x))))
        return(s)
      }

      TC_Sm <- lapply(fastalist, function(x) p(x[[1]], BSlict))
      TC_Sm_df <-
        do.call(rbind, TC_Sm)

      TC_Sm_df <-
        TC_Sm_df %>%
        as.data.frame(.) %>%
        set_rownames(names(TC_Sm)) %>%
        rownames_to_column("identifier")

      return(TC_Sm_df)
    }