R/generate_MSMS_table.R

In JustinZZW/LipLibBuild: LipLibBuild

#' @title generate_MSMS_table
#' @description  generate targeted MS/MS table for each compound
#' @author Zhiwei Zhou
#' \email{zhouzw@@sioc.ac.cn}
#' @param com.name Tompound name.
#' @param ext.mass The exact mass of compound.
#' @param mz The m/z value of adduct. If it inputted, the ext.mass will be replaced. Default: NULL
#' @param adduct The adduct form to dissociation, including "[M+H]", "[M+Na]", "[M+NH4]","[M-H]", "[M+HCOO]"
#' @param ce The collision energy. Default: 20V
#' @param charge The charge form of ion. Default: 1
#' @param rt The rt range of targeted ion. Default: ""
#' @param delta.rt The delta rt range. Default: ""
#' @param iso.width The isolation window, including: "Wide", "Medium", "Narrow"
#'
#' @example


generate_MSMS_table <- function(com.name,
                                ext.mass,
                                mz=NULL,
                                adduct=c("[M+H]", "[M+Na]", "[M+NH4]",
                                         "[M-H]", "[M+HCOO]"),
                                ce=20,
                                charge=1,
                                rt=0,
                                delta.rt=0.5,
                                iso.width=c("Wide",
                                            "Medium",
                                            "Narrow")
                                ){
  if (length(ext.mass)==0) {
    stop("Please input extact mass.\n")
  } else {
    ext.mass <- as.numeric(ext.mass)
  }

  options(warn = -1)

  ext.mass <- sapply(seq(length(adduct)), function(i){
    temp <- switch(adduct[i],
                   "[M+H]"={ext.mass+1.0078},
                   "[M+Na]"={ext.mass+22.9898},
                   "[M+NH4]"={ext.mass+18.0344},
                   "[M-H]"={ext.mass-1.0078},
                   "[M+HCOO]"={ext.mass+44.9977})
  })

  if (!is.null(mz)){
    ext.mass <- mz
  }

  iso.width <- switch (match.arg(iso.width),
                       "Wide"={"Wide (~9 m/z)"},
                       "Medium"={"Medium (~4 m/z)"},
                       "Narrow"={"Narrow (~1.3 m/z)"}
  )

  if (length(ce) > 1) {
    ce <- rep(ce, each=length(ext.mass))
  }

  result <- data.frame(V1=TRUE,
                       V2=ext.mass,
                       V3=charge,
                       V4=rt,
                       V5=delta.rt,
                       V6=iso.width,
                       V7=ce,
                       V8="",
                       stringsAsFactors = F
                       )

  temp <- c('On', 'Prec. m/z', 'Z', 'Ret. Time (min)', 'Time (min) Delta', 'Iso. Width', 'Collision Energy', 'Acquisition Time (ms/spec)')
  result <- rbind(c("TargetedMSMSTable", rep("", 7)), temp, result)
  colnames(result) <- ""

  temp <- paste(com.name, "csv", sep = ".")
  write.table(x = result,
              file = temp,
              sep = ",",
              row.names = F,
              col.names = F)

}


#' @title cal_ion_mz
#' @description  generate adducts mz
#' @author Zhiwei Zhou
#' \email{zhouzw@@sioc.ac.cn}
#' @param ext.mass The exact mass of compound.
#' @param name The name of csv file name. Default: "ext_mass_table.csv"
#' @example

cal_ion_mz <- function(ext.mass, name=NULL, is.output=FALSE){
  ext.mass.1 <- ext.mass+1.0078
  ext.mass.2 <- ext.mass+22.9898
  ext.mass.3 <- ext.mass+18.0344
  ext.mass.4 <- ext.mass-1.0078
  ext.mass.5 <- ext.mass+44.9977

  result <- data.frame(M=ext.mass,
                       'M+H'=ext.mass.1,
                       'M+Na'=ext.mass.2,
                       'M+NH4'=ext.mass.3,
                       'M-H'=ext.mass.4,
                       'M+HCOO'=ext.mass.5,
                       stringsAsFactors = F)

  temp <- c("M", "[M+H]", "[M+Na]", "[M+NH4]", "[M-H]", "[M+HCOO]")
  result <- rbind(temp, result)

  if (is.null(name)) {
    name <- "ext_mass_table.csv"
  } else {
    name <- paste(name, "csv", sep = ".")
  }

  if (is.output==TRUE){
    write.table(result,
                file = name,
                sep = ",",
                row.names = F,
                col.names = F)
  }

  result

}