R/get_confidence_stage4.R
In jaspershen/MSannotator: xMSannotator: R package for network based annotation of metabolomics data.
Defines functions
get_confidence_stage4
get_confidence_stage4 <-
function(curdata,max_diff_rt,adduct_weights=NA,filter.by=NA,min_ions_perchem=1,max_isp=5){
curdata<-curdata[order(curdata$Adduct),]
#return(curdata)
if(curdata$score[1]<0.1){
score_level<-0
final_res<-cbind(score_level,curdata)
final_res<-as.data.frame(final_res)
# final_res$score_level<-(as.numeric(as.factor(final_res$score_level)))
#print(final_res)
return(final_res)
}
curdata_all<-curdata
cur_adducts_with_isotopes<-curdata$Adduct
cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])",replacement="")
#cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\-[0-9]*\\])",replacement="")
if(is.na(adduct_weights)==TRUE){
data(adduct_table)
data(adduct_weights)
adduct_weights1<-matrix(nrow=2,ncol=2,0)
adduct_weights1[1,]<-c("M+H",1)
adduct_weights1[2,]<-c("M-H",1)
adduct_weights<-as.data.frame(adduct_weights1)
colnames(adduct_weights)<-c("Adduct","Weight")
}
adduct_monoisot<-data.frame(cbind("M",1,1,0,"-","S"))
colnames(adduct_monoisot)<-colnames(adduct_table)
adduct_table<-rbind(adduct_table,adduct_monoisot)
adduct_table<-adduct_table[order(adduct_table$Adduct),]
curdata<-cbind(curdata,cur_adducts)
curdata<-merge(curdata,adduct_table,by.x="cur_adducts",by.y="Adduct")
curdata<-curdata[,-c(1)]
#return(curdata)
formula_vec<-curdata$Formula
temp1<-curdata
temp1$Module_RTclust<-gsub(temp1$Module_RTclust,pattern="(_[0-9]*)",replacement="")
table_modules<-table(temp1$Module_RTclust)
rm(temp1)
module_names<-names(table_modules[which(table_modules>0)])
chemscoremat_conf_levels<-"High"
if(length(which(adduct_table$Adduct%in%cur_adducts))<1)
{
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}
if(length(unique(curdata$Adduct))<2 && curdata$score<10 && length(which(cur_adducts%in%filter.by))<1){
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}else{
if(length(unique(curdata$Adduct))<2 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Low"
# return(chemscoremat_conf_levels)
}
}
if(length(unique(curdata$Adduct))<2 && nrow(curdata)>1){
if(nrow(curdata)==2){
chemscoremat_conf_levels<-"Medium"
}
#return(chemscoremat_conf_levels)
if(length(which(cur_adducts%in%filter.by))<1)
{
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}
}
#print("Start")
curdata$time<-as.numeric(as.character(curdata$time))
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(delta_rt>max_diff_rt)
{
#chemscoremat_conf_levels<-"Medium"
#if(delta_rt>10){
chemscoremat_conf_levels<-"None"
#}
groupB<-group_by_rt(curdata,time_step=3,max.rt.diff=max_diff_rt,groupnum="")
groupB<-groupB[order(groupB$mz),]
cname1<-paste(groupB$mz,groupB$time,sep="_")
if(length(which(duplicated(cname1)==TRUE))>0){
groupB<-groupB[-which(duplicated(cname1)==TRUE),]
}
curdata<-curdata[order(curdata$mz),]
#print(curdata)
#print(groupB)
module_clust<-groupB[,1] #paste(curdata$module_num,groupB[,1],sep="")
curdata$Module_RTclust<-module_clust
#print("here")
#print(curdata)
if(length(which(adduct_weights[,1]%in%cur_adducts))>0 && curdata$score[1]>0.1)
{
if(is.na(filter.by)==TRUE){
good_mod<-curdata$Module_RTclust[which(curdata$Adduct%in%adduct_weights[,1])]
curdata<-curdata[which(curdata$Module_RTclust%in%good_mod),]
t1<-table(curdata$Module_RTclust)
t2<-t1[which(t1>0)]
t2<-t2[which(t2==max(t2)[1])]
n1<-names(t2)
curdata<-curdata[which(curdata$Module_RTclust==n1[1]),]
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(curdata$score[1]>0 && nrow(curdata)>1 && length(unique(curdata$Adduct))>1 && delta_rt<max_diff_rt){
chemscoremat_conf_levels<-"High"
}else{
chemscoremat_conf_levels<-"Low"
}
#print("here2")
}else{
if(length(which(cur_adducts%in%filter.by))>0){
good_mod<-curdata$Module_RTclust[which(curdata$Adduct%in%filter.by)]
curdata<-curdata[which(curdata$Module_RTclust%in%good_mod),]
curdata<-as.data.frame(curdata)
t1<-table(curdata$Module_RTclust)
t2<-t1[which(t1>0)]
t2<-t2[which(t2==max(t2)[1])]
n1<-names(t2)
curdata<-curdata[which(curdata$Module_RTclust==n1[1]),]
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(length(which(t1>1))<1){
if(curdata$score[1]>0 && nrow(curdata)>1 && length(unique(curdata$Adduct))>1 && delta_rt<max_diff_rt && length(which(curdata$Adduct%in%filter.by))>0){
chemscoremat_conf_levels<-"High"
}else{
if(curdata$score[1]>0 && length(which(curdata$Adduct%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
}else{
if(curdata$score[1]>0){
chemscoremat_conf_levels<-"Low"
}else{
chemscoremat_conf_levels<-"None"
}
}
}
}else{
t2<-t1[which(t1>0)]
t2<-t2[which(t2==max(t2)[1])]
n1<-names(t2)
curdata<-curdata[which(curdata$Module_RTclust==n1[1]),]
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(curdata$score[1]>0 && nrow(curdata)>1 && length(unique(curdata$Adduct))>1 && delta_rt<max_diff_rt && length(which(curdata$Adduct%in%filter.by))>0){
chemscoremat_conf_levels<-"High"
}else{
if(curdata$score[1]>0 && length(which(curdata$Adduct%in%filter.by))>0 && delta_rt<max_diff_rt){
chemscoremat_conf_levels<-"Medium"
}else{
if(curdata$score[1]>0){
chemscoremat_conf_levels<-"Low"
}else{
chemscoremat_conf_levels<-"None"
}
}
}
}
}
}
}
else{
#print(length(which(adduct_weights[,1]%in%cur_adducts)))
#print(curdata$score[1])
#print("here")
chemscoremat_conf_levels<-"None"
}
module_clust<-paste(curdata$module_num,curdata$Module_RTclust,sep="")
curdata$Module_RTclust<-module_clust
}
curdata<-as.data.frame(curdata)
#print("here 31")
#print(curdata)
temp1<-curdata
temp1$Module_RTclust<-gsub(temp1$Module_RTclust,pattern="(_[0-9]*)",replacement="")
table_modules<-table(temp1$Module_RTclust)
rm(temp1)
module_names<-names(table_modules[which(table_modules>0)])
#print("new mnames")
#print(module_names)
#print("OVER HERE")
#else
{
#change in 1.5.3
if(length(module_names)>1 && curdata$score<10){
chemscoremat_conf_levels<-"None"
}else{
if(length(module_names)>1 && curdata$score>10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
}
}
#else
{
if(nrow(curdata)<2)
{
#chemscoremat_conf_levels<-"Low"
if(length(which(cur_adducts%in%adduct_weights[,1]))<1){
chemscoremat_conf_levels<-"Low"
}else{
#matches an M+H and score is greater than 10
if(curdata$score>10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
}else{
chemscoremat_conf_levels<-"None"
}
}
}else{
min_nummol<-min(curdata$num_molecules)
min_nummol_ind<-which(curdata$num_molecules==min_nummol)
#num molecules check
if(min_nummol>1){
chemscoremat_conf_levels<-"Low"
}
else{
#Multiple molecules abundance check
check1<-gregexpr(text=cur_adducts,pattern="([2-3]+M)")
if(length(check1)>0)
{
#adduct_charges<-adduct_table[which(adduct_table$Adduct%in%cur_adducts),2]
min_mol<-min(curdata$num_molecules)
min_mol_ind<-which(curdata$num_molecules==min_mol)
max_int_min_mol<-max(curdata$mean_int_vec[min_mol_ind])
#max_int_min_charge<-max(curdata$mean_int_vec[min_mol_ind])
bad_ind_status<-rep(0,length(check1))
min_mol<-min(adduct_table[which(adduct_table$Adduct%in%cur_adducts),2])
#print("Max int")
#print(min_mol)
#print(max_int_min_mol)
if(min_mol<2)
{
#check pattern of each adduct
for(a1 in 1:length(check1))
{
strlength<-attr(check1[[a1]],"match.length")
#print(strlength)
if(strlength[1]>(-1))
{
#if(min_charge<2)
{
abund_ratio<-curdata$mean_int_vec[a1]/max_int_min_mol
#print("abund ratio is")
#print(abund_ratio)
if(is.na(abund_ratio)==FALSE){
if(abund_ratio>1){
bad_ind_status[a1]<-1
if(chemscoremat_conf_levels=="High"){
chemscoremat_conf_levels<-"Medium"
}else{
chemscoremat_conf_levels<-"Low"
}
}
}else{
chemscoremat_conf_levels<-"Low"
bad_ind_status[a1]<-1
}
}
}
}
if(length(which(bad_ind_status==1))>0){
#print(curdata)
#print(bad_ind_status)
bad_adducts<-cur_adducts[which(bad_ind_status==1)]
#curdata<-curdata[-which(bad_ind_status==1),]
#curdata<-curdata[-which(cur_adducts%in%bad_adducts),]
#print(curdata)
}
if(length(nrow(curdata)>0)){
cur_adducts_with_isotopes<-curdata$Adduct
#cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]\\])",replacement="")
# cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]*\\])",replacement="")
cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])",replacement="")
#cur_adducts<-gsub(cur_adducts,pattern="(_\\[\\-[0-9]*\\])",replacement="")
}else{
#print("here1")
chemscoremat_conf_levels<-"None"
}
}else{
#print("here1")
chemscoremat_conf_levels<-"Low"
}
#Multiply charged ions
#if(FALSE)
{
adduct_charges<-curdata$charge # adduct_table[which(adduct_table$Adduct%in%cur_adducts),3]
min_charge<-min(curdata$charge)
min_charge_ind<-which(curdata$charge==min_charge)
high_charge_ind<-which(curdata$charge>1)
max_int_min_charge<-max(curdata$mean_int_vec) #[min_charge_ind])
if(length(high_charge_ind)>0){
abund_ratio_min_maxcharge<-max(curdata$mean_int_vec[min_charge_ind])[1]/max(curdata$mean_int_vec[high_charge_ind])[1]
if((abund_ratio_min_maxcharge<1))
{
chemscoremat_conf_levels<-"Low"
}
}
bad_ind_status<-rep(1,length(check1))
if((min_charge>1))
{
chemscoremat_conf_levels<-"Low"
}
}
#isotope based check for +1 and +2 to make sure that the abundant form is present
check2<-gregexpr(text=cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])")
if(length(check2)>0){
for(a1 in 1:length(check2)){
strlength<-attr(check2[[a1]],"match.length")
if(strlength[1]>(-1)){
count_abundant_form<-length(which(cur_adducts%in%cur_adducts[a1]))
if(count_abundant_form<2)
{
#print("here")
#chemscoremat_conf_levels<-"None"
curdata<-curdata[-c(a1),]
}
}
}
}
cur_adducts_with_isotopes<-curdata$Adduct
#cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]\\])",replacement="")
# cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]*\\])",replacement="")
cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])",replacement="")
formula_vec<-curdata$Formula
curformula<-as.character(formula_vec[1])
# check2<-gregexpr(text=curformula,pattern="(_\\[\\+[3]\\])") #M+H+2
#print("HERE")
#print("here")
#print(chemscoremat_conf_levels)
#print(curdata)
if(FALSE){
check2<-gregexpr(text=cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])") #M+H_2
curformula<-gsub(curformula,pattern="Sr",replacement="")
curformula<-gsub(curformula,pattern="Sn",replacement="")
curformula<-gsub(curformula,pattern="Se",replacement="")
curformula<-gsub(curformula,pattern="Sc",replacement="")
curformula<-gsub(curformula,pattern="Sm",replacement="")
curformula<-gsub(curformula,pattern="(_\\[(\\+|\\-)[2]*\\])",replacement="")
if(length(check2)>0){
for(a1 in 1:length(check2)){
strlength<-attr(check2[[a1]],"match.length")
if(strlength[1]>(-1))
{
numchlorine<-check_element(curformula,"Cl")
numsulphur<-check_element(curformula,"S")
numbromine<-check_element(curformula,"Br")
max_isp_count<-max(numchlorine,numsulphur,numbromine)
if(is.na(max_isp_count)==TRUE | max_isp_count==0){
#chemscoremat_conf_levels<-"None"
curdata<-curdata[-c(a1),]
}else{
if(max_isp_count<1){
#chemscoremat_conf_levels<-"None"
curdata<-curdata[-c(a1),]
}
}
}
}
}
}
}
}
}
}
}
formula_vec<-curdata$Formula
curformula<-as.character(formula_vec[1])
curformula<-gsub(curformula,pattern="Ca",replacement="")
curformula<-gsub(curformula,pattern="Cl",replacement="")
curformula<-gsub(curformula,pattern="Cd",replacement="")
curformula<-gsub(curformula,pattern="Cr",replacement="")
numcarbons<-check_element(curformula,"C")
if(numcarbons<1){
chemscoremat_conf_levels<-"None"
}
if(length(unique(curdata$Adduct))<2 && nrow(curdata)>1){
if(nrow(curdata)==2){
chemscoremat_conf_levels<-"Medium"
}
#return(chemscoremat_conf_levels)
if(length(which(cur_adducts%in%filter.by))<1)
{
chemscoremat_conf_levels<-"None"
return(chemscoremat_conf_levels)
}
}else{
if(length(unique(curdata$Adduct))<2 && curdata$score<10 && length(which(cur_adducts%in%filter.by))<1){
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}else{
if(length(unique(curdata$Adduct))<2 && curdata$score>10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
# return(chemscoremat_conf_levels)
}else{
if(length(unique(curdata$Adduct))<2 && curdata$score<10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Low"
# return(chemscoremat_conf_levels)
}
}
}
}
if(nrow(curdata)<1){
score_level<-0
#curdata<-c(-1)
curdata<-curdata_all
}else{
#3: High
#2: medium
#1: Low
#0: None
score_level<-as.character(chemscoremat_conf_levels)
score_level<-gsub(score_level,pattern="High",replacement="3")
score_level<-gsub(score_level,pattern="Medium",replacement="2")
score_level<-gsub(score_level,pattern="Low",replacement="1")
score_level<-gsub(score_level,pattern="None",replacement="0")
}
if(is.na(score_level[1])==TRUE){
stop(curdata)
}
score_level<-as.numeric(as.character(score_level))
final_res<-cbind(score_level,curdata)
#print("curdata")
#print(curdata)
#print("score")
#print(score_level)
final_res<-as.data.frame(final_res)
# final_res$score_level<-(as.numeric(as.factor(final_res$score_level)))
#print(final_res)
#return(final_res)
if(length(which(is.na(final_res$score_level)==TRUE))>0){
final_res$score_level<-replace(final_res$score_level,which(is.na(final_res$score_level)==TRUE),0)
}
#final_res$score_level<-replace(final_res$score_level,which(final_res$score_level<1),0)
num_uniq_adducts<-length(unique(curdata$Adduct))
uniq_adducts<-unique(curdata$Adduct)
#num_good_adducts<-length(which(uniq_adducts%in%adduct_weights[,1]))
num_good_adducts<-length(which(uniq_adducts%in%filter.by))
#final_res$score<-(as.numeric(as.factor(final_res$score_level))^num_uniq_adducts)+0.1
#print(final_res$score)
#print(num_uniq_adducts)
#print(delta_rt)
#print(length(module_names))
if(num_good_adducts>0){
final_res$score<-final_res$score*num_good_adducts
}else{
final_res$score<-final_res$score*(0)
}
#final_res$score<-final_res$score*1*(0.9)*(1/((delta_rt*0.1)+1)^2)*num_uniq_adducts
# final_res$score<-final_res$score*(1/length(module_names))
#final_res$score<-(final_res$score)*(100)
#print("delta")
#print(delta_rt)
# if(final_res$chemical_ID=="C00073")
# {
#print(final_res)
#stop("Pyridoxine")
#stop("Methionine")
#}
#final_res$score_level<-as.numeric(as.character(final_res$score_level))
if(nrow(final_res)<min_ions_perchem){
final_res$score_level<-0 #max(1,final_res$score_level)
}
#print(final_res)
final_res<-as.data.frame(final_res)
return(final_res)
}
jaspershen/MSannotator documentation built on May 18, 2019, 5:55 p.m.
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Defines functions get_confidence_stage4
get_confidence_stage4 <-
function(curdata,max_diff_rt,adduct_weights=NA,filter.by=NA,min_ions_perchem=1,max_isp=5){
curdata<-curdata[order(curdata$Adduct),]
#return(curdata)
if(curdata$score[1]<0.1){
score_level<-0
final_res<-cbind(score_level,curdata)
final_res<-as.data.frame(final_res)
# final_res$score_level<-(as.numeric(as.factor(final_res$score_level)))
#print(final_res)
return(final_res)
}
curdata_all<-curdata
cur_adducts_with_isotopes<-curdata$Adduct
cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])",replacement="")
#cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\-[0-9]*\\])",replacement="")
if(is.na(adduct_weights)==TRUE){
data(adduct_table)
data(adduct_weights)
adduct_weights1<-matrix(nrow=2,ncol=2,0)
adduct_weights1[1,]<-c("M+H",1)
adduct_weights1[2,]<-c("M-H",1)
adduct_weights<-as.data.frame(adduct_weights1)
colnames(adduct_weights)<-c("Adduct","Weight")
}
adduct_monoisot<-data.frame(cbind("M",1,1,0,"-","S"))
colnames(adduct_monoisot)<-colnames(adduct_table)
adduct_table<-rbind(adduct_table,adduct_monoisot)
adduct_table<-adduct_table[order(adduct_table$Adduct),]
curdata<-cbind(curdata,cur_adducts)
curdata<-merge(curdata,adduct_table,by.x="cur_adducts",by.y="Adduct")
curdata<-curdata[,-c(1)]
#return(curdata)
formula_vec<-curdata$Formula
temp1<-curdata
temp1$Module_RTclust<-gsub(temp1$Module_RTclust,pattern="(_[0-9]*)",replacement="")
table_modules<-table(temp1$Module_RTclust)
rm(temp1)
module_names<-names(table_modules[which(table_modules>0)])
chemscoremat_conf_levels<-"High"
if(length(which(adduct_table$Adduct%in%cur_adducts))<1)
{
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}
if(length(unique(curdata$Adduct))<2 && curdata$score<10 && length(which(cur_adducts%in%filter.by))<1){
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}else{
if(length(unique(curdata$Adduct))<2 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Low"
# return(chemscoremat_conf_levels)
}
}
if(length(unique(curdata$Adduct))<2 && nrow(curdata)>1){
if(nrow(curdata)==2){
chemscoremat_conf_levels<-"Medium"
}
#return(chemscoremat_conf_levels)
if(length(which(cur_adducts%in%filter.by))<1)
{
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}
}
#print("Start")
curdata$time<-as.numeric(as.character(curdata$time))
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(delta_rt>max_diff_rt)
{
#chemscoremat_conf_levels<-"Medium"
#if(delta_rt>10){
chemscoremat_conf_levels<-"None"
#}
groupB<-group_by_rt(curdata,time_step=3,max.rt.diff=max_diff_rt,groupnum="")
groupB<-groupB[order(groupB$mz),]
cname1<-paste(groupB$mz,groupB$time,sep="_")
if(length(which(duplicated(cname1)==TRUE))>0){
groupB<-groupB[-which(duplicated(cname1)==TRUE),]
}
curdata<-curdata[order(curdata$mz),]
#print(curdata)
#print(groupB)
module_clust<-groupB[,1] #paste(curdata$module_num,groupB[,1],sep="")
curdata$Module_RTclust<-module_clust
#print("here")
#print(curdata)
if(length(which(adduct_weights[,1]%in%cur_adducts))>0 && curdata$score[1]>0.1)
{
if(is.na(filter.by)==TRUE){
good_mod<-curdata$Module_RTclust[which(curdata$Adduct%in%adduct_weights[,1])]
curdata<-curdata[which(curdata$Module_RTclust%in%good_mod),]
t1<-table(curdata$Module_RTclust)
t2<-t1[which(t1>0)]
t2<-t2[which(t2==max(t2)[1])]
n1<-names(t2)
curdata<-curdata[which(curdata$Module_RTclust==n1[1]),]
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(curdata$score[1]>0 && nrow(curdata)>1 && length(unique(curdata$Adduct))>1 && delta_rt<max_diff_rt){
chemscoremat_conf_levels<-"High"
}else{
chemscoremat_conf_levels<-"Low"
}
#print("here2")
}else{
if(length(which(cur_adducts%in%filter.by))>0){
good_mod<-curdata$Module_RTclust[which(curdata$Adduct%in%filter.by)]
curdata<-curdata[which(curdata$Module_RTclust%in%good_mod),]
curdata<-as.data.frame(curdata)
t1<-table(curdata$Module_RTclust)
t2<-t1[which(t1>0)]
t2<-t2[which(t2==max(t2)[1])]
n1<-names(t2)
curdata<-curdata[which(curdata$Module_RTclust==n1[1]),]
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(length(which(t1>1))<1){
if(curdata$score[1]>0 && nrow(curdata)>1 && length(unique(curdata$Adduct))>1 && delta_rt<max_diff_rt && length(which(curdata$Adduct%in%filter.by))>0){
chemscoremat_conf_levels<-"High"
}else{
if(curdata$score[1]>0 && length(which(curdata$Adduct%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
}else{
if(curdata$score[1]>0){
chemscoremat_conf_levels<-"Low"
}else{
chemscoremat_conf_levels<-"None"
}
}
}
}else{
t2<-t1[which(t1>0)]
t2<-t2[which(t2==max(t2)[1])]
n1<-names(t2)
curdata<-curdata[which(curdata$Module_RTclust==n1[1]),]
delta_rt<-max(curdata$time)-min(curdata$time)
delta_rt<-round(delta_rt)
if(curdata$score[1]>0 && nrow(curdata)>1 && length(unique(curdata$Adduct))>1 && delta_rt<max_diff_rt && length(which(curdata$Adduct%in%filter.by))>0){
chemscoremat_conf_levels<-"High"
}else{
if(curdata$score[1]>0 && length(which(curdata$Adduct%in%filter.by))>0 && delta_rt<max_diff_rt){
chemscoremat_conf_levels<-"Medium"
}else{
if(curdata$score[1]>0){
chemscoremat_conf_levels<-"Low"
}else{
chemscoremat_conf_levels<-"None"
}
}
}
}
}
}
}
else{
#print(length(which(adduct_weights[,1]%in%cur_adducts)))
#print(curdata$score[1])
#print("here")
chemscoremat_conf_levels<-"None"
}
module_clust<-paste(curdata$module_num,curdata$Module_RTclust,sep="")
curdata$Module_RTclust<-module_clust
}
curdata<-as.data.frame(curdata)
#print("here 31")
#print(curdata)
temp1<-curdata
temp1$Module_RTclust<-gsub(temp1$Module_RTclust,pattern="(_[0-9]*)",replacement="")
table_modules<-table(temp1$Module_RTclust)
rm(temp1)
module_names<-names(table_modules[which(table_modules>0)])
#print("new mnames")
#print(module_names)
#print("OVER HERE")
#else
{
#change in 1.5.3
if(length(module_names)>1 && curdata$score<10){
chemscoremat_conf_levels<-"None"
}else{
if(length(module_names)>1 && curdata$score>10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
}
}
#else
{
if(nrow(curdata)<2)
{
#chemscoremat_conf_levels<-"Low"
if(length(which(cur_adducts%in%adduct_weights[,1]))<1){
chemscoremat_conf_levels<-"Low"
}else{
#matches an M+H and score is greater than 10
if(curdata$score>10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
}else{
chemscoremat_conf_levels<-"None"
}
}
}else{
min_nummol<-min(curdata$num_molecules)
min_nummol_ind<-which(curdata$num_molecules==min_nummol)
#num molecules check
if(min_nummol>1){
chemscoremat_conf_levels<-"Low"
}
else{
#Multiple molecules abundance check
check1<-gregexpr(text=cur_adducts,pattern="([2-3]+M)")
if(length(check1)>0)
{
#adduct_charges<-adduct_table[which(adduct_table$Adduct%in%cur_adducts),2]
min_mol<-min(curdata$num_molecules)
min_mol_ind<-which(curdata$num_molecules==min_mol)
max_int_min_mol<-max(curdata$mean_int_vec[min_mol_ind])
#max_int_min_charge<-max(curdata$mean_int_vec[min_mol_ind])
bad_ind_status<-rep(0,length(check1))
min_mol<-min(adduct_table[which(adduct_table$Adduct%in%cur_adducts),2])
#print("Max int")
#print(min_mol)
#print(max_int_min_mol)
if(min_mol<2)
{
#check pattern of each adduct
for(a1 in 1:length(check1))
{
strlength<-attr(check1[[a1]],"match.length")
#print(strlength)
if(strlength[1]>(-1))
{
#if(min_charge<2)
{
abund_ratio<-curdata$mean_int_vec[a1]/max_int_min_mol
#print("abund ratio is")
#print(abund_ratio)
if(is.na(abund_ratio)==FALSE){
if(abund_ratio>1){
bad_ind_status[a1]<-1
if(chemscoremat_conf_levels=="High"){
chemscoremat_conf_levels<-"Medium"
}else{
chemscoremat_conf_levels<-"Low"
}
}
}else{
chemscoremat_conf_levels<-"Low"
bad_ind_status[a1]<-1
}
}
}
}
if(length(which(bad_ind_status==1))>0){
#print(curdata)
#print(bad_ind_status)
bad_adducts<-cur_adducts[which(bad_ind_status==1)]
#curdata<-curdata[-which(bad_ind_status==1),]
#curdata<-curdata[-which(cur_adducts%in%bad_adducts),]
#print(curdata)
}
if(length(nrow(curdata)>0)){
cur_adducts_with_isotopes<-curdata$Adduct
#cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]\\])",replacement="")
# cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]*\\])",replacement="")
cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])",replacement="")
#cur_adducts<-gsub(cur_adducts,pattern="(_\\[\\-[0-9]*\\])",replacement="")
}else{
#print("here1")
chemscoremat_conf_levels<-"None"
}
}else{
#print("here1")
chemscoremat_conf_levels<-"Low"
}
#Multiply charged ions
#if(FALSE)
{
adduct_charges<-curdata$charge # adduct_table[which(adduct_table$Adduct%in%cur_adducts),3]
min_charge<-min(curdata$charge)
min_charge_ind<-which(curdata$charge==min_charge)
high_charge_ind<-which(curdata$charge>1)
max_int_min_charge<-max(curdata$mean_int_vec) #[min_charge_ind])
if(length(high_charge_ind)>0){
abund_ratio_min_maxcharge<-max(curdata$mean_int_vec[min_charge_ind])[1]/max(curdata$mean_int_vec[high_charge_ind])[1]
if((abund_ratio_min_maxcharge<1))
{
chemscoremat_conf_levels<-"Low"
}
}
bad_ind_status<-rep(1,length(check1))
if((min_charge>1))
{
chemscoremat_conf_levels<-"Low"
}
}
#isotope based check for +1 and +2 to make sure that the abundant form is present
check2<-gregexpr(text=cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])")
if(length(check2)>0){
for(a1 in 1:length(check2)){
strlength<-attr(check2[[a1]],"match.length")
if(strlength[1]>(-1)){
count_abundant_form<-length(which(cur_adducts%in%cur_adducts[a1]))
if(count_abundant_form<2)
{
#print("here")
#chemscoremat_conf_levels<-"None"
curdata<-curdata[-c(a1),]
}
}
}
}
cur_adducts_with_isotopes<-curdata$Adduct
#cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]\\])",replacement="")
# cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[\\+[0-9]*\\])",replacement="")
cur_adducts<-gsub(cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])",replacement="")
formula_vec<-curdata$Formula
curformula<-as.character(formula_vec[1])
# check2<-gregexpr(text=curformula,pattern="(_\\[\\+[3]\\])") #M+H+2
#print("HERE")
#print("here")
#print(chemscoremat_conf_levels)
#print(curdata)
if(FALSE){
check2<-gregexpr(text=cur_adducts_with_isotopes,pattern="(_\\[(\\+|\\-)[0-9]*\\])") #M+H_2
curformula<-gsub(curformula,pattern="Sr",replacement="")
curformula<-gsub(curformula,pattern="Sn",replacement="")
curformula<-gsub(curformula,pattern="Se",replacement="")
curformula<-gsub(curformula,pattern="Sc",replacement="")
curformula<-gsub(curformula,pattern="Sm",replacement="")
curformula<-gsub(curformula,pattern="(_\\[(\\+|\\-)[2]*\\])",replacement="")
if(length(check2)>0){
for(a1 in 1:length(check2)){
strlength<-attr(check2[[a1]],"match.length")
if(strlength[1]>(-1))
{
numchlorine<-check_element(curformula,"Cl")
numsulphur<-check_element(curformula,"S")
numbromine<-check_element(curformula,"Br")
max_isp_count<-max(numchlorine,numsulphur,numbromine)
if(is.na(max_isp_count)==TRUE | max_isp_count==0){
#chemscoremat_conf_levels<-"None"
curdata<-curdata[-c(a1),]
}else{
if(max_isp_count<1){
#chemscoremat_conf_levels<-"None"
curdata<-curdata[-c(a1),]
}
}
}
}
}
}
}
}
}
}
}
formula_vec<-curdata$Formula
curformula<-as.character(formula_vec[1])
curformula<-gsub(curformula,pattern="Ca",replacement="")
curformula<-gsub(curformula,pattern="Cl",replacement="")
curformula<-gsub(curformula,pattern="Cd",replacement="")
curformula<-gsub(curformula,pattern="Cr",replacement="")
numcarbons<-check_element(curformula,"C")
if(numcarbons<1){
chemscoremat_conf_levels<-"None"
}
if(length(unique(curdata$Adduct))<2 && nrow(curdata)>1){
if(nrow(curdata)==2){
chemscoremat_conf_levels<-"Medium"
}
#return(chemscoremat_conf_levels)
if(length(which(cur_adducts%in%filter.by))<1)
{
chemscoremat_conf_levels<-"None"
return(chemscoremat_conf_levels)
}
}else{
if(length(unique(curdata$Adduct))<2 && curdata$score<10 && length(which(cur_adducts%in%filter.by))<1){
chemscoremat_conf_levels<-"None"
#return(chemscoremat_conf_levels)
}else{
if(length(unique(curdata$Adduct))<2 && curdata$score>10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Medium"
# return(chemscoremat_conf_levels)
}else{
if(length(unique(curdata$Adduct))<2 && curdata$score<10 && length(which(cur_adducts%in%filter.by))>0){
chemscoremat_conf_levels<-"Low"
# return(chemscoremat_conf_levels)
}
}
}
}
if(nrow(curdata)<1){
score_level<-0
#curdata<-c(-1)
curdata<-curdata_all
}else{
#3: High
#2: medium
#1: Low
#0: None
score_level<-as.character(chemscoremat_conf_levels)
score_level<-gsub(score_level,pattern="High",replacement="3")
score_level<-gsub(score_level,pattern="Medium",replacement="2")
score_level<-gsub(score_level,pattern="Low",replacement="1")
score_level<-gsub(score_level,pattern="None",replacement="0")
}
if(is.na(score_level[1])==TRUE){
stop(curdata)
}
score_level<-as.numeric(as.character(score_level))
final_res<-cbind(score_level,curdata)
#print("curdata")
#print(curdata)
#print("score")
#print(score_level)
final_res<-as.data.frame(final_res)
# final_res$score_level<-(as.numeric(as.factor(final_res$score_level)))
#print(final_res)
#return(final_res)
if(length(which(is.na(final_res$score_level)==TRUE))>0){
final_res$score_level<-replace(final_res$score_level,which(is.na(final_res$score_level)==TRUE),0)
}
#final_res$score_level<-replace(final_res$score_level,which(final_res$score_level<1),0)
num_uniq_adducts<-length(unique(curdata$Adduct))
uniq_adducts<-unique(curdata$Adduct)
#num_good_adducts<-length(which(uniq_adducts%in%adduct_weights[,1]))
num_good_adducts<-length(which(uniq_adducts%in%filter.by))
#final_res$score<-(as.numeric(as.factor(final_res$score_level))^num_uniq_adducts)+0.1
#print(final_res$score)
#print(num_uniq_adducts)
#print(delta_rt)
#print(length(module_names))
if(num_good_adducts>0){
final_res$score<-final_res$score*num_good_adducts
}else{
final_res$score<-final_res$score*(0)
}
#final_res$score<-final_res$score*1*(0.9)*(1/((delta_rt*0.1)+1)^2)*num_uniq_adducts
# final_res$score<-final_res$score*(1/length(module_names))
#final_res$score<-(final_res$score)*(100)
#print("delta")
#print(delta_rt)
# if(final_res$chemical_ID=="C00073")
# {
#print(final_res)
#stop("Pyridoxine")
#stop("Methionine")
#}
#final_res$score_level<-as.numeric(as.character(final_res$score_level))
if(nrow(final_res)<min_ions_perchem){
final_res$score_level<-0 #max(1,final_res$score_level)
}
#print(final_res)
final_res<-as.data.frame(final_res)
return(final_res)
}
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