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)
}
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