R/kideraFactors.R

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

#' @export kideraFactors
#' @importFrom utils data
#' @title Compute the Kidera factors of a protein sequence
#' @description The Kidera Factors were originally derived by applying multivariate analysis to 188 physical properties of the 20 amino acids and using dimension reduction techniques. This function calculates the average of the ten Kidera factors for a protein sequence.
#' @param seq An amino-acids sequence
#' @return A list with the average of the ten Kidera factors. 
#' The first four factors are essentially pure physical properties; the remaining six factors are superpositions of several physical properties, and are labelled for convenience by the name of the most heavily weighted component.
#' \itemize{
#' \item{KF1:} Helix/bend preference,
#' \item{KF2:} Side-chain size,
#' \item{KF3:} Extended structure preference,
#' \item{KF4:} Hydrophobicity,
#' \item{KF5:} Double-bend preference,
#' \item{KF6:} Partial specific volume,
#' \item{KF7:} Flat extended preference,
#' \item{KF8:} Occurrence in alpha region,
#' \item{KF9:} pK-C,
#' \item{KF10:} Surrounding hydrophobicity}
#' @references Kidera, A., Konishi, Y., Oka, M., Ooi, T., & Scheraga, H. A. (1985). Statistical analysis of the physical properties of the 20 naturally occurring amino acids. Journal of Protein Chemistry, 4(1), 23-55.
#' @examples 
#' kideraFactors(seq = "KLKLLLLLKLK")
#' # [[1]]
#' #     KF1         KF2         KF3         KF4         KF5 
#' # -0.78545455  0.29818182 -0.23636364 -0.08181818  0.21000000 
#' #     KF6         KF7         KF8         KF9        KF10 
#' # -1.89363636  1.02909091 -0.51272727  0.11181818  0.81000000 

kideraFactors <- function (seq) {
  
  # Remove the break lines from the sequence and Split by amino acids
  seq <- aaCheck(seq)
  
  # Load the KFactors data
  factors <- AAdata$kideraFactors
  
  # Compute the selected Kidera factor.
  kFactors <- lapply(seq, function(seq) {
    sapply(names(factors), function(factor) {
      (sum(factors[[factor]][seq], na.rm = TRUE) / length(seq))
    })
  })
  
  # Return
  return(kFactors)
}