R/createNet.R

In BASiNET: Classification of RNA Sequences using Complex Network Theory

#'@title Creates an untargeted graph from a biological sequence
#'@name createNet
#'
#'@description A function that from a biological sequence generates a graph not addressed having as words vertices, this being able to have its size parameter set by the' word 'parameter. The connections between words depend of the' step 'parameter that indicates the next connection to be formed
#'
#'@param step It is the integer parameter that decides the step that will be taken to make a new connection
#'@param word This integer parameter decides the size of the word that will be formed
#'@param sequence It is a vector that represents the sequence
#'
#'
#'@return Returns the non-directed graph formed through the sequence
#'
#' @author Eric Augusto Ito
#'
#'

createNet <- function(word, step, sequence){
	aux<-""
	index<-1
	position<-0
	cont<-length(sequence)
	comma<-0
	x<-0
	k<-1
	vector<-c()

	while((index-1+(word*2))<cont){

		while(x<word){
			aux<-paste(aux,sequence[index],sep="");
			x<-x+1;
			index<-index+1;
		}
		vector<-c(vector,aux)
		aux<-""
		x<-0;
		while(x<word){

			aux<-paste(aux,sequence[index],sep="");
			x<-x+1;
			index<-index+1;
		}
		vector<-c(vector,aux)
		aux<-""
		x<-0;
		position<-position+step;
		index<-position+1;
	}
	net<-graph <- graph(edges=vector,directed=FALSE)

	return(net)
}