R/calculate_ions.R

In yuriychen/MSPlotcyl: MS spectrum plot

calculate_byions <- function(pep_seq, cal_ion_list=cal_ion_list){
  pep_seq_list <- unlist(strsplit(pep_seq,''))

  b_ions <- c(cal_ion_list['Hp',1])
  y_ions <- c((cal_ion_list['HOH',1] + cal_ion_list['Hp',1]))

  for (i in pep_seq_list) {
    b_ions <- append(b_ions,(b_ions[(length(b_ions))] + cal_ion_list[i,1]))
  }

  for (i in rev(pep_seq_list)){
    y_ions <- append(y_ions,(y_ions[(length(y_ions))] + cal_ion_list[i,1]))
  }

  b_ions <- b_ions[-1]
  b_ions <- data.frame(b_ions)
  b_ions$ion <- paste('b',rownames(b_ions),sep = '')
  colnames(b_ions) <- c('mz','ion')
  y_ions <- y_ions[-1]
  y_ions <- data.frame(y_ions)
  y_ions$ion <- paste('y',rownames(y_ions),sep = '')
  colnames(y_ions) <- c('mz','ion')
  df_ions <- rbind(b_ions,y_ions)

  return(df_ions)
}