R/frequency.R

In Ant-nguyen/RmuMotif: Useful functions to help find motifs in DNA sequences.

#' FrequencyMap
#'
#' Extract frequency of specific kmers (snippets of specific length) from a larger sequence.
#'
#' @param k An Integer representing length of kmer
#' @param txt A character string of DNA sequence
#' @return A List of frequency of kmers in txt sequence, Class of object is frequencyMap allowing
#' for specifc plot method.
#' @export
frequencyMap <- function(k,txt){ # k is an integer value representing a length of sequence (kmer)
  freq <- list()
  n <- nchar(txt)-k+1
  for(i in 1:n){
    x <- (k+i-1)
    pattern <- substr(txt,i,x)
    freq[[pattern]] <- patternCount(pattern,txt)
  }
  class(freq) <-"frequencyMap"  #classify end result to frequencyMap, allowing specific plotting
  return(freq)
}