R/DNAanalysis_additional-fxns.R

In allisondavis/DNAanalysis_PACKAGE: An introduction to DNA analysis

#' @title CG content function
#' @description This function allows you calculate the fraction of C and G content of a specified sequence.
#' @param sequence a single vector of individual character
#' @param wordsize the length of characters to include in nucleotide "word" search; for CG this is 2
#' @param alphabet all characters within the seqence to analyze
#' @keywords CG
#' @export
#' @examples
#' CG(FISHsequence, wordsize= 2, alphabet= c("a", "c", "t", "g"))


CG <- function(sequence) {

  tot <- seqinr::count(sequence, wordsize = 2, alphabet = s2c("acgt"))
  cg <- tot[7]
  freq <- cg/sum(tot[1],tot[2],tot[3],tot[4],tot[5],tot[6],tot[7],tot[8],tot[9],tot[10],tot[11],tot[12],tot[13],tot[14],tot[15], tot[16])
  print(freq)

}

#' @title Sliding Widow Plot- GC content
#' @description This function allows you create a sliding window plot of GC content within a specified sequence; originally created by Avril Coghlan, from Little Book of R
#' @param inputseq a single vector of individual character
#' @param windowsize number of nucleotide sequences in a single step
#' @keywords swp
#' @export
#' @examples
#' swp.GC(100, FISHsequence)

#' GC
swp.GC <- function(windowsize, inputseq)
{
  starts <- seq(1, length(inputseq)-windowsize, by = windowsize)
  n <- length(starts)
  chunkGCs <- NULL
  for (i in 1:n) {
    chunk <- inputseq[starts[i]:(starts[i]+windowsize-1)]
    chunkGC <- seqinr::GC(chunk)
    chunkGCs[i] <- chunkGC
  }
  plot(starts,chunkGCs,type="b",xlab="Nucleotide start position",ylab="GC content")
}

#' @title Sliding Widow Plot-CG content
#' @description This function allows you create a sliding window plot of CG content within a specified sequence; originally created by Avril Coghlan, from Little Book of R and modified with our CG function
#' @param inputseq a single vector of individual character
#' @param windowsize number of nucleotide sequences in a single step
#' @keywords swp
#' @export
#' @examples
#' swp.CG(100, FISHsequence)

#' CG
swp.CG <- function(windowsize, inputseq)
{
  starts <- seq(1, length(inputseq)-windowsize, by = windowsize)
  n <- length(starts)
  chunkCGs <- NULL
  for (i in 1:n) {
    chunk <- inputseq[starts[i]:(starts[i]+windowsize-1)]
    chunkCG <- CG(chunk)
    chunkCGs[i] <- chunkCG
  }
  plot(starts,chunkCGs,type="b",xlab="Nucleotide start position",ylab="CG content")
}