R/SequentialSparse.R

In ProteinDescriptors: Generates Various Protein Descriptors for Machine Learning Algorithms

#' Sequential sparse descriptor.
#'
#' \code{SequentialSparse} returns the concatenation of sparse descriptors of
#' amino acids in a protein sequence.
#'
#' @param x A string of amino acid letters
#' @return A 20*n dimensional numeric vector where n is the protein length
#'
#' @export SequentialSparse
#'
#' @examples
#' x = "LALHLLLLHMHMMDRSLLLH"
#' SequentialSparse(x)


SequentialSparse<-function(x)
{

n=nchar(x)
x=unlist(strsplit(x, split = ""))

   sparse = t(data.frame(
	A = c(1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
	R = c(0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
	N = c(0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
	D = c(0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
	C = c(0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
	E = c(0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
	Q = c(0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0),
    	G = c(0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0),
	H = c(0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0),
	I = c(0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0),
	L = c(0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0),
	K = c(0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0),
	M = c(0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0),
	F = c(0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0),
    	P = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0),
	S = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0),
	T = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0),
	W = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0),
	Y = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0),
	V = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1)))


result<-c()
for(i in 1:n)
{
result<-c(result,(sparse[rownames(sparse)==x[i]]))
}

return(result)
}