R/516-extractPCMDescScales.R

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

#' Scales-Based Descriptors with 20+ classes of Molecular Descriptors
#'
#' Scales-Based Descriptors with 20+ classes of Molecular Descriptors
#'
#' This function calculates the scales-based descriptors with 
#' molecular descriptors sets calculated by
#' Dragon, Discovery Studio and MOE.
#' Users could specify which molecular descriptors to select from one of these 
#' deseriptor sets by specify the numerical or character index of the 
#' molecular descriptors in the descriptor set.
#' 
#' @param x A character vector, as the input protein sequence.
#' @param propmat The matrix containing the descriptor set for the amino acids, 
#'        which could be chosen from 
#'        \code{AAMOE2D}, \code{AAMOE3D}, \code{AACPSA},
#'        \code{AADescAll}, \code{AA2DACOR}, \code{AA3DMoRSE},
#'        \code{AAACF}, \code{AABurden}, \code{AAConn}, 
#'        \code{AAConst}, \code{AAEdgeAdj}, \code{AAEigIdx}, 
#'        \code{AAFGC}, \code{AAGeom}, \code{AAGETAWAY}, 
#'        \code{AAInfo}, \code{AAMolProp}, \code{AARandic}, 
#'        \code{AARDF}, \code{AATopo}, \code{AATopoChg}, 
#'        \code{AAWalk}, \code{AAWHIM}.
#' @param index Integer vector or character vector. Specify which molecular 
#'        descriptors to select from one of these deseriptor sets by specify the 
#'        numerical or character index of the molecular descriptors in the 
#'        descriptor set. 
#'        Default is \code{NULL}, means selecting all the molecular descriptors 
#'        in this descriptor set.
#' @param pc Integer. The maximum dimension of the space which the data 
#'        are to be represented in.
#'        Must be no greater than the number of AA properties provided.
#' @param lag The lag parameter. Must be less than the amino acids.
#' @param scale Logical. Should we auto-scale the property matrix 
#'        (\code{propmat}) before doing MDS? Default is \code{TRUE}.
#' @param silent Logical. Whether we print the standard deviation, 
#'        proportion of variance and the cumulative proportion of 
#'        the selected principal components or not.
#'        Default is \code{TRUE}.
#'
#' @return A length \code{lag * p^2} named vector, 
#'         \code{p} is the number of scales selected.
#' 
#' @keywords extract scales extrPCMDescScales PCM
#'
#' @aliases extrPCMDescScales
#' 
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>, 
#'         Nan Xiao <\url{http://r2s.name}>
#' 
#' @seealso See \code{\link{extrPCMScales}} for generalized 
#' AA-descriptor based scales descriptors.
#' 
#' @export extrPCMDescScales
#' 
#' @examples
#' x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
#' descscales = extrPCMDescScales(x, propmat = 'AATopo', index = c(37:41, 43:47), 
#'                                   pc = 5, lag = 7, silent = FALSE)
#' 

extrPCMDescScales = function (x, propmat, index = NULL, pc, lag, 
                                 scale = TRUE, silent = TRUE) {

    propmat = get(propmat)
    if (!is.null(index)) propmat = propmat[, index]

    result = extrPCMScales(x = x, propmat = propmat, pc = pc, lag = lag, 
                              scale = scale, silent = silent)

    return(result)

}