R/get_mz_by_monoisotopicmass.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

#' get_mz_by_monoisotopicmass
#' 
#' Generate list of expected m/z for a specific monoisotopic mass
#' 
#' 
#' @param monoisotopicmass Monoisotopic mass. e.g.: 149.051
#' @param dbid Database or user-defined ID. e.g.: "M001"
#' @param name Metabolite name. e.g.: "Methionine"
#' @param formula Chemical formula. e.g.: "C5H11NO2S"
#' @param queryadductlist List of adducts to be used for searching.  eg:
#' c("M+H","M+Na","M+K"), c("positive") for positive adducts, c("negative") for
#' negative adducts c("all") for all adducts
#' @param syssleep Wait time between queries to prevent overloading the KEGG
#' REST interface. e.g.: 0.1
#' @return Returns an R object with a list of expected m/z for the input
#' monoisotopic mass.
#' @author Karan Uppal
get_mz_by_monoisotopicmass <- function(monoisotopicmass, 
    dbid = NA, name = NA, formula = NA, queryadductlist = c("M+H"), 
    syssleep = 0.01, adduct_table = NA) {
    cnames <- c("mz", "ID", "Name", "Formula", "MonoisotopicMass", 
        "Adduct", "AdductMass")
    
    
    if (is.na(adduct_table) == TRUE) {
        
        try(rm(adduct_table), silent = TRUE)
    }
    # if(is.na(adduct_table)==TRUE)
    {
        data(adduct_table)
        adduct_table <- as.data.frame(adduct_table)
    }
    
    # adduct_table<-read.table('/Users/karanuppal/Documents/Emory/JonesLab/Projects/xMSannotator/adduct_table.txt',sep='\t',header=TRUE)
    # adduct_table<-adduct_table[c(which(adduct_table[,6]=='S'),which(adduct_table[,6]=='Acetonitrile')),]
    
    adduct_names <- as.character(adduct_table[, 1])
    adductlist <- adduct_table[, 4]
    mult_charge <- adduct_table[, 3]
    num_mol <- adduct_table[, 2]
    names(adductlist) <- as.character(adduct_names)
    names(mult_charge) <- as.character(adduct_names)
    names(num_mol) <- as.character(adduct_names)
    alladducts <- adduct_names
    
    
    if (queryadductlist[1] == "positive") {
        queryadductlist <- adduct_names[which(adduct_table[, 
            5] == "positive")]
        
    } else {
        if (queryadductlist[1] == "negative") {
            
            queryadductlist <- adduct_names[which(adduct_table[, 
                5] == "negative")]
            
        } else {
            if (queryadductlist[1] == "all") {
                
                
                queryadductlist <- alladducts
                
                
            } else {
                if (length(which(queryadductlist %in% alladducts == 
                  FALSE)) > 0) {
                  
                  errormsg <- paste("Adduct should be one of:", 
                    sep = "")
                  for (i in alladducts) {
                    errormsg <- paste(errormsg, i, sep = " ; ")
                  }
                  stop(errormsg, "\n\nUsage: feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"M+H\", \"M+Na\"), xMSannotator.outloc, numnodes=1)", 
                    "\n\n OR  feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"positive\"), xMSannotator.outloc, numnodes=1)", 
                    "\n\n OR  feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"negative\"), xMSannotator.outloc, numnodes=1)", 
                    "\n\n OR  feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"all\"), xMSannotator.outloc, numnodes=1)")
                }
                
            }
        }
    }
    
    map_res <- {
    }
    
    if (is.na(dbid) == TRUE) {
        dbid = "-"
    }
    
    if (is.na(name) == TRUE) {
        name = "-"
    }
    if (is.na(formula) == TRUE) {
        formula = "-"
    }
    
    exact_mass <- monoisotopicmass
    
    
    for (adnum in 1:length(queryadductlist)) {
        adductname = queryadductlist[adnum]
        adductmass = adductlist[as.character(adductname)]
        adductcharge = mult_charge[as.character(adductname)]
        adductnmol = num_mol[as.character(adductname)]
        
        # mz=((adductnmol*exact_mass)+(adductmass))/(adductcharge))
        
        mz = ((exact_mass * as.numeric(adductnmol)) + (as.numeric(adductmass)))/as.numeric(adductcharge)
        
        # delta_ppm=(max.mz.diff)*(mz/1000000)
        # min_mz=round((mz-delta_ppm),5)
        # max_mz=round((mz+delta_ppm),5)
        res = {
        }
        mzorig = round(exact_mass, 5)
        # delta_ppm=round(delta_ppm,5)
        
        syssleep1 <- (syssleep/5)
        Sys.sleep(syssleep1)
        
        
        cur_map_res <- cbind(mz, dbid, name, formula, adductname, 
            adductmass, mzorig)
        cur_map_res <- as.data.frame(cbind(mz, as.character(dbid), 
            as.character(name), as.character(formula), mzorig, 
            adductname, adductmass))
        # print(cur_map_res)
        cur_map_res <- as.data.frame(cur_map_res)
        map_res <- rbind(map_res, cur_map_res)
        
    }
    
    
    colnames(map_res) <- cnames
    
    map_res <- unique(map_res)
    map_res <- as.data.frame(map_res)
    
    return(map_res)
}