R/getscore.R

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

getscore <- function(k, mchemdata, chemids, corthresh, global_cor, 
    mzid, max_diff_rt, level_module_isop_annot, adduct_table, 
    adduct_weights, mass_defect_window = 0.01, mass_defect_mode = "pos") {
    
    chemscoremat <- {
    }
    chemid <- chemids[k]
    curmchemdata <- mchemdata[which(mchemdata$chemical_ID == 
        chemid), ]
    rm(mchemdata)
    rm(chemids)
    curmchemdata <- as.data.frame(curmchemdata)
    
    # level_module_isop_annot<-level_module_isop_annot[which(level_module_isop_annot$mz
    
    chem_score <- get_chemscorev1.6.71(chemicalid = chemid, 
        mchemicaldata = curmchemdata, corthresh = corthresh, 
        global_cor, mzid, max_diff_rt = max_diff_rt, level_module_isop_annot = level_module_isop_annot, 
        adduct_table = adduct_table, adduct_weights = adduct_weights, 
        mass_defect_window = mass_defect_window, mass_defect_mode = mass_defect_mode)
    
    if (length(chem_score) > 0) {
        if (chem_score$chemical_score >= (-100)) {
            
            
            
            chem_score$filtdata <- chem_score$filtdata[order(chem_score$filtdata$mz), 
                ]
            
            chemscoremat <- cbind(chem_score$chemical_score, 
                chem_score$filtdata)
            rm(chem_score)
            
            chemscoremat <- na.omit(chemscoremat)
            chemscoremat <- as.data.frame(chemscoremat)
            
        }
    } else {
        rm(chem_score)
    }
    
    return(chemscoremat)
}