R/kmerScan.R

In WubingZhang/PhageR: Functions for phage display data analysis

#' Count k-mer from reads
#'
#' @docType methods
#' @name kmerScan
#' @rdname kmerScan
#'
#' @param count Count matrix of peptides.
#' @param kmer An integer.
#'
#' @return Count matrix for k-mer motif.
#'
#' @author Wubing Zhang
#' @import data.table
#' @export
#'
kmerScan <- function(count, kmer = 5){
  require(data.table)
  peplen = nchar(rownames(count)[1])
  if(kmer>=peplen) return(count)
  peptides_k = unlist(lapply(kmer:peplen, function(y){
    substr(rownames(count), y-kmer+1, y)
  }))
  peptides_k = matrix(peptides_k, ncol = nrow(count), byrow = TRUE)
  colnames(peptides_k) = rownames(count)
  tmp = as.data.frame(stack(peptides_k))
  tmp = cbind.data.frame(tmp, count[tmp$col,])
  tmp = setDT(tmp)
  newcount = tmp[, lapply(.SD, sum), .SDcols = colnames(tmp)[4:ncol(tmp)], by = value]
  newcount = as.data.frame(newcount, stringsAsFactors = FALSE)
  rownames(newcount) = newcount$value;
  newcount = newcount[,-1]
  return(newcount)
}