#' @export stScales
#' @title Compute the ST-scales of a protein sequence
#' @description ST-scales were proposed by Yang et al, taking 827 properties into account which are mainly constitutional, topological, geometrical, hydrophobic, elec- tronic, and steric properties of a total set of 167 AAs.
#' @references Yang, L., Shu, M., Ma, K., Mei, H., Jiang, Y., & Li, Z. (2010). ST-scale as a novel amino acid descriptor and its application in QSAM of peptides and analogues. Amino acids, 38(3), 805-816.
#' @param seq An amino-acids sequence
#' @return The computed average of ST-scales of all the amino acids in the corresponding peptide sequence.
#' @examples stScales(seq = "QWGRRCCGWGPGRRYCVRWC")
#' # [[1]]
#' # ST1 ST2 ST3 ST4 ST5 ST6 ST7 ST8
#' # -0.63760 0.07965 0.05150 0.07135 -0.27905 -0.80995 0.58020 0.54400
stScales <- function(seq){
# Split the sequence by amino-acids - Remove spaces and line breaks
seq <- aaCheck(seq)
# Load the ST-scales
scales <- AAdata$stScales
# Computes the ST-scales for given sequences
lapply(seq, function(seq) {
sapply(names(scales), function(scale) {
(sum(scales[[scale]][seq], na.rm = TRUE) / length(seq))
})
})
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.