R/GetMonoPeptideFrequency.R

In crarlus/paprbag: Pathogenicity Prediction of Bacterial Genomes

#' @title Get the Frequency of each amino acid
#' @description Get the Frequency of each amino acid
#' @param Seq An AAStringSet object
#' @param prob Should relative frequncies be returned
#' @return A data.frame object containing the frequencies (columns) for the submitted sequences (rows)
#' @author Carlus Deneke
GetMonoPeptideFrequency <- function(Seq,prob=F){

  #require(Biostrings)
  # AAfreq <- Biostrings::alphabetFrequency(Seq,as.prob=prob)[,1:27]
  # colnames(AAfreq) <- paste("MonoPep",colnames(AAfreq),sep="_")
  # colnames(AAfreq)[27] <- paste("MonoPep","terminal",sep="_")
  # rownames(AAfreq) <- names(Seq)

  AAfreq <- Biostrings::alphabetFrequency(Seq,as.prob=prob)
  AAfreq <- AAfreq[,c(intersect(colnames(AAfreq),AA_STANDARD),"*")]

  colnames(AAfreq)[colnames(AAfreq) == "*"] <- "terminal"
  colnames(AAfreq) <- paste("MonoPep",colnames(AAfreq),sep="_")

  rownames(AAfreq) <- names(Seq)


  return(AAfreq)
}