R/pcm-02-extractDescScales.R

In road2stat/protr: Generating Various Numerical Representation Schemes for Protein Sequences

#' 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 can 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 can 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}, and \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}, which 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
#' amino acid 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.
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export extractDescScales
#'
#' @examples
#' x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
#' descscales <- extractDescScales(
#'   x,
#'   propmat = "AATopo", index = c(37:41, 43:47),
#'   pc = 5, lag = 7, silent = FALSE
#' )
extractDescScales <- function(
  x, propmat, index = NULL, pc, lag, scale = TRUE, silent = TRUE) {
  propmat <- get(propmat)
  if (!is.null(index)) propmat <- propmat[, index]

  res <- extractScales(
    x = x, propmat = propmat, pc = pc, lag = lag, scale = scale, silent = silent
  )

  res
}