R/check_golden_rules.R

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

check_golden_rules <- function(curformula, NOPS_check = FALSE) {
    
    
    numnitrogens <- check_element(curformula, "N")
    numcarbons <- check_element(curformula, "C")
    
    numoxygens <- check_element(curformula, "O")
    
    numhydrogens <- check_element(curformula, "H")
    
    numphos <- check_element(curformula, "P")
    numsulphur <- check_element(curformula, "S")
    
    
    
    if (numcarbons < 1) {
        
        bool_check <- 0
    } else {
        
        max_hydrogens <- (2 * numcarbons) + numnitrogens + 
            2
        
        nitrogen_to_carbon_ratio <- numnitrogens/numcarbons
        
        oxygen_to_carbon_ratio <- numoxygens/numcarbons
        
        phosphorus_to_carbon_ratio <- numphos/numcarbons
        
        sulphur_to_carbon_ratio <- numsulphur/numcarbons
        
        hydrogens_to_carbon_ratio <- numhydrogens/numcarbons
        
        bool_check <- 1
        
        
        
        if (hydrogens_to_carbon_ratio < 0.1 | hydrogens_to_carbon_ratio > 
            6) {
            
            bool_check = 0
        }
        
        if (nitrogen_to_carbon_ratio > 4) {
            
            bool_check = 0
        }
        
        if (oxygen_to_carbon_ratio > 3) {
            
            bool_check = 0
        }
        
        if (phosphorus_to_carbon_ratio > 2) {
            
            bool_check = 0
        }
        
        if (sulphur_to_carbon_ratio > 3) {
            
            bool_check = 0
        }
        
        if (NOPS_check == TRUE) {
            # NOPS>1
            if (numnitrogens > 1 & numoxygens > 1 & numphos > 
                1 & numsulphur > 1) {
                if (numnitrogens > 10 | numoxygens > 20 | 
                  numphos > 4 | numsulphur > 3) {
                  
                  bool_check <- 0
                }
                
            }
            
            
            # NOP>3
            if (numnitrogens > 3 & numoxygens > 3 & numphos > 
                3) {
                if (numnitrogens > 11 | numoxygens > 22 | 
                  numphos > 6) {
                  
                  bool_check <- 0
                }
                
            }
            
            # OPS>1
            if (numoxygens > 1 & numphos > 1 & numsulphur > 
                1) {
                if (numoxygens > 14 | numphos > 3 | numsulphur > 
                  3) {
                  
                  bool_check <- 0
                }
                
            }
            
            # PSN>1
            if (numnitrogens > 1 & numphos > 1 & numsulphur > 
                1) {
                if (numnitrogens > 4 | numphos > 3 | numsulphur > 
                  3) {
                  
                  bool_check <- 0
                }
                
            }
            
            # NOS>6
            if (numnitrogens > 6 & numoxygens > 6 & numsulphur > 
                6) {
                if (numnitrogens > 19 | numoxygens > 14 | 
                  numsulphur > 8) {
                  
                  bool_check <- 0
                }
                
            }
            
        }
        
        
    }
    res <- cbind(curformula, bool_check)
    res <- as.data.frame(res)
    
    
    return(res)
    
}