R/412-extractProtQSO.R

In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

#' Quasi-Sequence-Order (QSO) Descriptor
#'
#' Quasi-Sequence-Order (QSO) Descriptor
#'
#' This function calculates the Quasi-Sequence-Order (QSO) descriptor
#' (Dim: \code{20 + 20 + (2 * nlag)}, default is 100).
#'
#' @param x A character vector, as the input protein sequence.
#'
#' @param nlag The maximum lag, defualt is 30.
#'
#' @param w The weighting factor, default is 0.1.
#'
#' @return A length \code{20 + 20 + (2 * nlag)} named vector
#'
#' @seealso See \code{\link{extractProtSOCN}}
#' for sequence-order-coupling numbers.
#'
#' @export extractProtQSO
#'
#' @references
#' Kuo-Chen Chou. Prediction of Protein Subcellar Locations by
#' Incorporating Quasi-Sequence-Order Effect.
#' \emph{Biochemical and Biophysical Research Communications},
#' 2000, 278, 477-483.
#'
#' Kuo-Chen Chou and Yu-Dong Cai. Prediction of Protein Sucellular Locations by
#' GO-FunD-PseAA Predictor.
#' \emph{Biochemical and Biophysical Research Communications},
#' 2004, 320, 1236-1239.
#'
#' Gisbert Schneider and Paul Wrede. The Rational Design of
#' Amino Acid Sequences by Artifical Neural Networks and Simulated
#' Molecular Evolution: Do Novo Design of an Idealized Leader Cleavge Site.
#' \emph{Biophys Journal}, 1994, 66, 335-344.
#'
#' @examples
#' x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
#' extractProtQSO(x)
#'

extractProtQSO = function (x, nlag = 30, w = 0.1) {

    if (checkProt(x) == FALSE) stop('x has unrecognized amino acid type')

    N = nchar(x)
    if (N <= nlag) stop('Length of the protein sequence must be greater than "nlag"')

    DistMat1 = read.csv(system.file('sysdata/Schneider-Wrede.csv', package = 'Rcpi'), header = TRUE)
    DistMat2 = read.csv(system.file('sysdata/Grantham.csv', package = 'Rcpi'), header = TRUE)
    row.names(DistMat1) = as.character(DistMat1[, 1])
    DistMat1 = DistMat1[, -1]
    row.names(DistMat2) = as.character(DistMat2[, 1])
    DistMat2 = DistMat2[, -1]

    xSplitted = strsplit(x, split = '')[[1]]

    # Compute Schneider.tau_d

    tau1 = vector('list', nlag)

    for (d in 1:nlag) {
        for (i in 1:(N - d)) {
            tau1[[d]][i] = (DistMat1[xSplitted[i], xSplitted[i + d]])^2
        }
    }

    tau1 = sapply(tau1, sum)

    # Compute Grantham.tau_d

    tau2 = vector('list', nlag)

    for (d in 1:nlag) {
        for (i in 1:(N - d)) {
            tau2[[d]][i] = (DistMat2[xSplitted[i], xSplitted[i + d]])^2
        }
    }

    tau2 = sapply(tau2, sum)

    # Compute fr

    AADict = c('A', 'R', 'N', 'D', 'C', 'E', 'Q', 'G', 'H', 'I',
               'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V')

    fr = summary(factor(xSplitted, levels = AADict), maxsum = 21)

    # Compute Schneider.Xr Grantham.Xr Schneider.Xd Grantham.Xd

    Xr1 = fr/(1 + (w * sum(tau1)))
    names(Xr1) = paste('Schneider.Xr.', names(Xr1), sep = '')

    Xr2 = fr/(1 + (w * sum(tau2)))
    names(Xr2) = paste('Grantham.Xr.', names(Xr2), sep = '')

    Xd1 = (w * tau1)/(1 + (w * sum(tau1)))
    names(Xd1) = paste('Schneider.Xd.', 1:nlag, sep = '')

    Xd2 = (w * tau2)/(1 + (w * sum(tau2)))
    names(Xd2) = paste('Grantham.Xd.', 1:nlag, sep = '')

    QSO = c(Xr1, Xr2, Xd1, Xd2)

    return(QSO)

}