R/517-extractPCMPropScalesGap.R

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

#' Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)
#' with Gap Support
#'
#' Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)
#' with Gap Support
#'
#' This function calculates amino acid properties based scales descriptors
#' (protein fingerprint) with gap support. Users could specify which AAindex
#' properties to select from the AAindex database by specify the numerical or
#' character index of the properties in the AAindex database.
#'
#' @param x A character vector, as the input protein sequence.
#'        Use '\code{-}' to represent gaps in the sequence.
#' @param index Integer vector or character vector. Specify which AAindex
#'        properties to select from the AAindex database by specify the
#'        numerical or character index of the properties in the
#'        AAindex database.
#'        Default is \code{NULL}, means selecting all the AA properties
#'        in the AAindex database.
#' @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
#'        before PCA? 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 (principal components) selected.
#'
#' @keywords extract scales AAindex gap
#'
#' @aliases extrProtFPGap
#'
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>, 
#'         Nan Xiao <\url{http://r2s.name}>
#'
#' @export extrProtFPGap
#'
#' @examples
#' # amino acid sequence with gaps
#' x = readFASTA(system.file('protseq/align.fasta', package = 'BioMedR'))$`IXI_235`
#' fp = extrProtFPGap(x, index = c(160:165, 258:296), pc = 5, lag = 7, silent = FALSE)
#'

extrProtFPGap = function (x, index = NULL, pc, lag,
                             scale = TRUE, silent = TRUE) {
  
  AAindex = get('AAindex')
  
  if (!is.null(index)) propmat = t(na.omit(as.matrix(AAindex[index, 7:26])))
  
  result = extrPCMScaleGap(x = x, propmat = propmat, pc = pc, lag = lag, scale = scale, silent = silent)
  
  return(result)
  
}