R/read_modifications.R

In zym530902730/rplot: Visualization of modified and unmodified peptide spectra pairs for determination of modification positions in R

#' @author Yiming Zhao
#'
#' @title read_modifications
#'
#' @description read modifications.xml file

#' @param xmlurl modifications.xml file path
#' @param modifications modifications

#' @return modifications

#' @import stringr
#' @import xml2
#' @importFrom utils read.table
#' @export


read_modifications <-function(xmlurl,modifications){
  # xmlread = read_xml(xmlurl)
  # f1 = xml_find_all(xmlread,"//modifications/modification")
  # f2 = xml_find_all(xmlread,"//modifications/modification/modification_site")
  # modfication = xml_attr(f1,"composition")
  # mod = xml_attr(f1,"title")
  # mod = substr(mod,1,2)
  # mod = tolower(mod)
  # Modified_amino_acids = xml_attr(f2,"site")
  # 
  # modifications = cbind(modfication,mod,Modified_amino_acids)
  # modifications = data.frame(modifications)
    xmlread = read_xml(xmlurl)
    xpath = paste("//modification[@title='",modifications,"']",sep = "")
    f1 = xml_find_all(xmlread,xpath)
    f2 = xml_find_all(f1,"modification_site")
    modfication = xml_attr(f1,"composition")
    mod = xml_attr(f1,"title")
    mod = substr(mod,1,2)
    mod = tolower(mod)
    Modified_amino_acids = xml_attr(f2,"site")
    
    modifications = cbind(modfication,mod,Modified_amino_acids)
    modifications = data.frame(modifications)
    
  return(modifications)
}