R/get_mz_by_KEGGcompoundIDs.R

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

get_mz_by_KEGGcompoundIDs <-
function(keggIDs,queryadductlist=c("M+H"),syssleep=0.01){
    cnames<-c("mz","chemical_ID", "Name", "Formula", "MonoisotopicMass", "Adduct","AdductMass")
    
    #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<-{}
    for(i in 1:length(keggIDs)){
        
        Sys.sleep(syssleep)
        
        keggID<-keggIDs[i]
        #print(keggID)
        keggID<-paste(keggID,collapse="")
        kegglink<-paste("<a href=http://www.genome.jp/dbget-bin/www_bget?cpd:",keggID,">",keggID,"</a>",sep="")
        
        
        
        search_link=paste("http://rest.kegg.jp/get/cpd:",as.character(keggID),sep="")
        
        d2<-try(read.delim(search_link,header=FALSE),silent=TRUE)
        
        if(is(d2,"try-error")){
            next
        }else{
            
            dm<-keggGet(paste("cpd:",keggID,sep=""))
            
            formula<-dm[[1]]$FORMULA
            chem_name<-paste(dm[[1]]$NAME,collapse="")
            
            exact_mass<-as.numeric(dm[[1]]$EXACT_MASS)
            
            if(length(exact_mass)>0){
                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)]
                    
                    
                    #mono_mass=((mz.val*adduct_charge)-(adductmass))/(adductnmol)
                    
                    mz=((exact_mass*adductnmol)+(adductmass))/adductcharge
                    
                    
              
                    
                    syssleep1<-(syssleep/5)
                    Sys.sleep(syssleep1)
                    
                    
                    cur_map_res<-c(mz,keggID,chem_name,formula,mzorig,adductname,adductmass)
                    map_res<-rbind(map_res,cur_map_res)
                    
                }
            }else{
                cur_map_res<-c("-",keggID,chem_name,"-","-","-","-")
                map_res<-rbind(map_res,cur_map_res)
            }
            
        }
        
        
        
        
        #colnames(map_res)<-cnames
        
    }
    map_res<-unique(map_res)
    map_res<-as.data.frame(map_res)
     map_res<-map_res[,c(1:6)]
     colnames(map_res)<-c("mz","KEGG.Compound.ID","Name","Formula","MonoisotopicMass","Adduct")
    return(map_res)
    
    
}