R/pcm-01-extractScalesGap.R

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

.protcheckgap <- function(x) {
  AADict <- c(
    "A", "R", "N", "D", "C", "E", "Q", "G", "H", "I",
    "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V",
    "-"
  )

  all(strsplit(x, split = "")[[1]] %in% AADict)
}

#' Scales-Based Descriptors derived by Principal Components Analysis
#' (with Gap Support)
#'
#' This function calculates scales-based descriptors
#' derived by Principal Components Analysis (PCA), with gap support.
#' Users can provide customized amino acid property matrices.
#' This function implements the core computation procedure needed for
#' the scales-based descriptors derived by AA-Properties (AAindex)
#' and scales-based descriptors derived by 20+ classes of 2D and 3D
#' molecular descriptors (Topological, WHIM, VHSE, etc.) in the protr package.
#'
#' @param x A character vector, as the input protein sequence.
#' Use '\code{-}' to represent gaps in the sequence.
#' @param propmat A matrix containing the properties for the amino acids.
#' Each row represent one amino acid type, each column represents
#' one property. Note that the one-letter row names must be provided
#' for we need them to seek the properties for each AA type.
#' @param pc Integer. Use the first pc principal components as the scales.
#' 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 PCA? Default is \code{TRUE}.
#' @param silent Logical. Whether to 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 (principal components) selected.
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{extractProtFPGap}} for amino acid property based
#' scales descriptors (protein fingerprint) with gap support.
#'
#' @importFrom stats prcomp predict
#'
#' @export extractScalesGap
#'
#' @examples
#' # amino acid sequence with gaps
#' x <- readFASTA(system.file("protseq/align.fasta", package = "protr"))$`IXI_235`
#' data(AAindex)
#' AAidxmat <- t(na.omit(as.matrix(AAindex[, 7:26])))
#' scales <- extractScalesGap(x, propmat = AAidxmat, pc = 5, lag = 7, silent = FALSE)
extractScalesGap <- function(
    x, propmat, pc, lag, scale = TRUE, silent = TRUE) {
  if (.protcheckgap(x) == FALSE) {
    stop('x has unrecognized amino acid types. Note: use "-" to represent gaps.')
  }

  gapmat <- t(matrix(rep(0L, ncol(propmat))))
  row.names(gapmat) <- "-"
  propmat <- rbind(propmat, gapmat)

  pc <- min(pc, ncol(propmat), nrow(propmat))

  prop.pr <- prcomp(propmat, scale = scale)
  prop.pred <- predict(prop.pr)

  accmat <- matrix(0, pc, nchar(x))
  x.split <- strsplit(x, "")[[1]]

  for (i in 1:nchar(x)) accmat[, i] <- prop.pred[x.split[i], 1:pc]

  res <- acc(accmat, lag)

  if (!silent) {
    cat("Summary of the first", pc, "principal components:", "\n")
    print(summary(prop.pr)$importance[, 1:pc])
  }

  res
}