R/601-getCPI.R

In road2stat/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

.inner = function (a, b, f, ...) {

    # For computing column-by-column (pseudo)-tensor product type interactions

    f = match.fun(f)
    apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))

}

.getCPICombine = function (drugmat, protmat) {

    return(cbind(drugmat, protmat))

}

.getCPITensor = function (drugmat, protmat, row, dcol, pcol) {

    return(array(.inner(t(drugmat), protmat, '*'), c(row, dcol * pcol)))

}

#' Generating Compound-Protein Interaction Descriptors
#'
#' Generating Compound-Protein Interaction Descriptors
#'
#' This function calculates the compound-protein interaction descriptors
#' by three types of interaction:
#' \itemize{
#' \item \code{combine} - combine the two descriptor matrix,
#' result has \code{(p1 + p2)} columns
#' \item \code{tensorprod} - calculate column-by-column
#' (pseudo)-tensor product type interactions, result has
#' \code{(p1 * p2)} columns
#' }
#'
#' @param drugmat The compound descriptor matrix.
#' @param protmat The protein descriptor matrix.
#' @param type The interaction type, one or two of
#' \code{"combine"} and \code{"tensorprod"}.
#'
#' @return A matrix containing the compound-protein interaction descriptors
#'
#' @seealso See \code{\link{getPPI}} for generating
#' protein-protein interaction descriptors.
#'
#' @export getCPI
#'
#' @examples
#' x = matrix(1:10, ncol = 2)
#' y = matrix(1:15, ncol = 3)
#'
#' getCPI(x, y, 'combine')
#' getCPI(x, y, 'tensorprod')
#' getCPI(x, y, type = c('combine', 'tensorprod'))
#' getCPI(x, y, type = c('tensorprod', 'combine'))
#'

getCPI = function (drugmat, protmat, type = c('combine', 'tensorprod')) {

    if (!is.matrix(drugmat)) drugmat = as.matrix(drugmat)
    if (!is.matrix(protmat)) protmat = as.matrix(protmat)

    drugrow = nrow(drugmat)
    protrow = nrow(protmat)

    if (drugrow != protrow) stop('Matrix row count must match')

    drugcol = ncol(drugmat)
    protcol = ncol(protmat)

    if (missing(type)) stop('Must provide at least one interaction type')

    if (all(type == 'combine')) {

        result = .getCPICombine(drugmat, protmat)

    } else if (all(type == 'tensorprod')) {

        result = .getCPITensor(drugmat, protmat, row = drugrow,
                               dcol = drugcol, pcol = protcol)

    } else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {

        result = cbind(.getCPICombine(drugmat, protmat),
                       .getCPITensor(drugmat, protmat, row = drugrow,
                                     dcol = drugcol, pcol = protcol))

    } else {

        stop('Interaction type must be in "tensorprod" and "combine" or both')

    }

    return(result)

}