R/cldetect.R
In yguitton/MeHaloCoA: Fast identification of Cl or Br containing compounds in LC-MS
#new version 14/07/2014 with check in FUN2 for multiple m/z hits
#change in M1 M2 calculation it was ppm this is confusing pepole ask for 50ppm error and in fact the soft used 60 ppmerr
cldetect<-
function(outdir="",xsAnnotate,plotps=TRUE, deprof=FALSE, Thresh=30, m1=1.0030, m2=1.997, mdiff=0.05, ppmerr=50, val="into", mdiff2=0.001, myfile="halo_list.csv",myfile2="halo_list_short.csv", m1need=FALSE){
if (!class(xsAnnotate) == "xsAnnotate") {
if(class(xsAnnotate)=="list"){
if(length(which(lapply(an,function(x)class(x))=="xsAnnotate"))>=1){
xsAnnotate<-xsAnnotate[[as.vector(which(lapply(an,function(x)class(x))=="xsAnnotate"))]]
}
else{
stop("Parameter object is no xsAnnotate object\n")
}
}
else{
stop("Parameter object is no xsAnnotate object\n")
}
}
#find output directory
path<-outdir
if ((path != "") == FALSE) {
#require(tcltk)
path=tclvalue(tkchooseDirectory(title="Please, select your Results directory"))
}
an=xsAnnotate
#find pspectrum with 2 Da neutral loss for Chlorine, Bromine it is ok
hits <- findNeutralLossSpecs(an, mzdiff=m2, mzabs=mdiff, mzppm=ppmerr)
good<-which(hits==TRUE)
#Find M+2 isotope and its intensity and compare to M+1 and M intensities into can be changed by maxo with val option
funM2<-function(target, massadduct1=m1, massadduct2=m2, mzabs=mdiff, ppmerr=ppmerr, Thresh=Thresh, val=val){
ls_halogenated<-list()
ls_Mlist<-list()
ls_test<-list()
M<-peak[which(peak[,"mz"]==target),val]
M1<-subset(peak,peak[,1]<=(ppm(target,ppmerr,l=TRUE)[1]+massadduct1) & (ppm(target,ppmerr,l=TRUE)[2]+massadduct1)<=peak[,1])#+ 10 ppm error pour le m+2 en limite haute
M2<-subset(peak,peak[,1]<=(ppm(target,ppmerr,l=TRUE)[1]+massadduct2) & (ppm(target,ppmerr,l=TRUE)[2]+massadduct2)<=peak[,1])
#test if several M1 or M2[,"mz"]
if (length(M1[,"mz"])>1){
testvect<-M1[,"mz"]
M1<-M1[which(abs(testvect-target-massadduct1)==min(abs(testvect-target-massadduct1))),]
}
if (length(M2[,"mz"])>1){
testvect<-M2[,"mz"]
M2<-M2[which(abs(testvect-target-massadduct2)==min(abs(testvect-target-massadduct2))),]
}
if (length(M2[,"mz"])!=0){
#Si M+1 et M+2 OK
if ( length(M1[,"mz"])!=0){
test2<-(peak[which(peak[,"mz"]==M2[,"mz"]),val]*100)/peak[which(peak[,"mz"]==target),val][1]
test1<-(peak[which(peak[,"mz"]==M1[,"mz"]),val]*100)/peak[which(peak[,"mz"]==target),val][1]
print(paste("Tests Result for target=",target, "and pcgroup=",good[j]))
print(test2)
print(test1)
#liste des tests
#test1<150 is to avoid peaking M+1 isotopes as a M
if ((test2>=Thresh) && (test1<150) && (test2<600)){
if((M1[,"mz"]-target)[1]>=massadduct1-mzabs){
Halo1<-"OK"
}else
{
Halo1<-"No"
}
if((M2[,"mz"]-target)[1]<=massadduct2+mzabs){
Halo2<-"OK"
}else
{
Halo2<-"No"
}
if(Halo1=="OK" && Halo2=="OK" ){
Halo3<-"OK"
}else
{
Halo3<-"No"
}
if(Halo3=="OK" && test2>90 ){
Br<-"OK"
}else
{
Br<-"No"
}
if(Halo3=="OK" && test2>Thresh ){
Cl<-"OK"
}else
{
Cl<-"No"
}
RT<-round(median(getpspectra(an, grp=as.vector(good)[j])[, "rt"])/60,3)
if (Halo2=="OK"){
cat(j,good[j],RT,M,target,M1[,"mz"][1],M2[,"mz"][1],(M1[,"mz"]-target)[1],(M2[,"mz"]-target)[1],test1[1],test2[1],Halo3,Br,Cl,"\n", file = zz, sep = ",")
ls_halogenated<-good[j]
}
}
}
if(m1need==FALSE){
#Si M+2 OK mais pas M+1 (pas assez intense)
if ( length(M1[,"mz"])==0){
test2<-(peak[which(peak[,"mz"]==M2[,"mz"]),val]*100)/peak[which(peak[,"mz"]==target),val][1]
test1<-"TOO LOW"
#list des test
if ((test2>=Thresh) && (test2<600)){
Halo1<-"M+1 Too Low"
Halo3<-"M+1 Too Low"
Br<-"M+1 Too Low"
Cl<-"M+1 Too Low"
if((M2[,"mz"]-target)[1]<=massadduct2+mzabs){
Halo2<-"OK"
}else
{
Halo2<-"No"
}
RT<-round(median(getpspectra(an, grp=as.vector(good)[j])[, "rt"])/60,3)
if (Halo2=="OK"){
cat(j,good[j],RT,M,target,M1[,"mz"][1],M2[,"mz"][1],(M1[,"mz"]-target)[1],(M2[,"mz"]-target)[1],test1[1],test2[1],Halo3,Br,Cl,"\n", file = zz, sep = ",")
ls_halogenated<-good[j]
}
}
}
}#end if M+1 available
}
if (length(ls_halogenated)!=0){
# reslist<-list("ls_halogenated"=ls_halogenated, "ls_Mlist"=ls_Mlist, "ls_test"=ls_test)
# return(reslist)
return(ls_halogenated)
}
}# end funM2
#j in long = lenght good
zz<-file(file.path(path,myfile), "w")
cat("j","pcgroup","RT","Intensity","M","M1","M2","M1-M","M2-M","M1/M","M2/M","MassDefect filters OK","Br","Cl","\n", file = zz, sep = ",")
ls_good<-list()
if(length(good)!=0){
for (j in 1:length(good)){
ls_target<-list()
peak<-getpspectra(an, good[j])
#remove NaN containing lignes
peak<-peak[complete.cases(peak), ]
if (deprof==TRUE){
options(warn=-1)
if(require(RMassBank)){
peak<-RMassBank::deprofile.scan(peak[,c("mz",val)])
colnames(peak)<-c("mz",val)
options(warn=0)
}else{
stop("Couldn't load RMassBank")
}
}
#ls_target<-peak[sort.list(peak[,"into"], decreasing=TRUE), ][,1]
ls_target<-peak[,1]
ls_halogenated<-lapply(ls_target, function(x)funM2(target=x, massadduct1=m1, massadduct2=m2, mzabs=mdiff, ppmerr=ppmerr, Thresh=Thresh, val=val))
#ls_halogenated
ls_good[[j]]<-peak[which(match(ls_halogenated,good[j])==1),"mz"]
}
}else{
print("No peak")
}
close(zz)
data<-read.table(file.path(path,myfile),header=TRUE, sep=",")
clvect<-unique(data[which(data[,"Cl"]=="OK"),"pcgroup"])
brvect<-unique(data[which(data[,"Br"]=="OK"),"pcgroup"])
ls_good2<-lapply(ls_good,function(x)length(x))
print(ls_good2)
if (plotps==TRUE && length(good[which(ls_good2>=1)])>=1){
#outdirbasicGCplot for outputs just to keep track off the name
outdirbasicGCplot<-file.path(path,paste("EICs_Results_",format(Sys.time(), "%Y_%B_%d_%Hh%M"),sep=""))
#plot pspectra and EICs for good peaks
basicGCplot(outdir=path,xsAnnotate=an,pspecrange= as.vector(good[which(ls_good2>=1)]), check="")
}
if (length(good[which(ls_good2>=1)])>=1){
#if bug change an@xcmsSet@filepaths<-"path to your file"
#Plot IFC
#matrix1 with ls_good list m/z +/- mdiff2
matrix1<-cbind((unlist(ls_good[which(ls_good2>=1)])-mdiff2),(unlist(ls_good[which(ls_good2>=1)])+mdiff2))
mzrange<-matrix(ncol=2, data=matrix1)
print(dim(matrix1))
#1- faire max int de chque pcgroup (peut-etre lors des tests dans fichier final) attention xs = xcmsSet or cldetect accepte seulment le an voir getEICs from CAMERA
peakT<-getPeaklist(an) #peak table
malist<-NULL #start at NULL
for (i in 1:dim(mzrange)[1]){
malist<-c(malist,which(peakT[,"mz"]>mzrange[i,1] & peakT[,"mz"]<mzrange[i,2]))
# print(i) #debug
}
EIC.matrix<-getAllPeakEICs(an,index=rep(1,nrow(an@groupInfo)))
EIC.matrix$EIC[!is.finite(EIC.matrix$EIC)]<-0
#gestion du cas ou is.null(dim(EIC.matrix$EIC[malist,])) ou colSums ne fonctionne pas
if(!is.null(dim(EIC.matrix$EIC[malist,]))){
plot(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC[malist,])+max(colSums(EIC.matrix$EIC))*0.05, type="l", ylim=c(0,max(colSums(EIC.matrix$EIC))),col="Red", main=paste("IFC for \n",basename(an@xcmsSet@filepaths)), xlab="seconds", ylab="Intensity") #IFC
points(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC), type="l", col="grey") # TIC
legend("topright", legend=c("IFC","TIC","Highly Interesting Point"), lty=1, lwd=2, col=c("red","grey","blue"), bty="n")
}else
{
plot(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC), type="l", col="grey", main=paste("IFC for \n",basename(an@xcmsSet@filepaths), "\n Note a problem exists!"), xlab="seconds", ylab="Intensity") #IFC
}
#mat a refaire si plotps=False
rt<-list()
cl<-list()
br<-list()
for(i in 1:length(as.vector(good[which(ls_good2>=1)]))){
rt[i] <- round(median(getpspectra(an, grp=as.vector(good[which(ls_good2>=1)])[i])[, "rt"])/60,3)
cl[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], clvect))
br[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], brvect))
}
mat<-data.frame(cbind(as.numeric(rt),cl,br,lapply(ls_good[which(ls_good2>=1)], FUN=function(x)paste0(round(as.numeric(x),3), collapse="|"))))
colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
mat<-mat[sort.list(unlist(mat[,"RT"]),decreasing = FALSE), ]
#gestion du cas ou length(which(mat[,"Cl OK"]=="TRUE"))<1
if (length(which(mat[,"Cl OK"]=="TRUE"))>=1){
arrows(as.numeric(mat[which(mat[,"Cl OK"]=="TRUE"),"RT"])*60, x1=as.numeric(mat[which(mat[,"Cl OK"]=="TRUE"),"RT"])*60, y0=max(colSums(EIC.matrix$EIC))*0.05, y1=0,col = "blue", lty = "solid", lwd = 2, length = 0.04, angle = 45, code = 1)
}
}else
{
EIC.matrix<-getAllPeakEICs(an,index=rep(1,nrow(an@groupInfo)))
EIC.matrix$EIC[!is.finite(EIC.matrix$EIC)]<-0
plot(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC), type="l", col="grey", main=paste("IFC for \n",basename(an@xcmsSet@filepaths), "\n No Cl or Br"), xlab="seconds", ylab="Intensity") #IFC
}
if (length(good[which(ls_good2>=1)])>=1){
cat("Nan Mais Halo Quoi!,\n Good News, putative chlorinated compound found \n")
cat(paste("Results files are in", outdir))
if (plotps==TRUE){
print(paste("EICs and Mass Spectra are in ",outdirbasicGCplot, sep=""), sep="")
return(mat)
}else{
#return(ls_good[which(ls_good2>=1)])
#Now for RTs for all peaks in the whole an list()
rt<-list()
cl<-list()
br<-list()
for(i in 1:length(as.vector(good[which(ls_good2>=1)]))){
rt[i] <- round(median(getpspectra(an, grp=as.vector(good[which(ls_good2>=1)])[i])[, "rt"])/60,3)
cl[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], clvect))
br[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], brvect))
}
mat<-data.frame(cbind(as.numeric(rt),cl,br,lapply(ls_good[which(ls_good2>=1)], FUN=function(x)paste0(round(as.numeric(x),3), collapse="|"))))
colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
mat<-mat[sort.list(unlist(mat[,"RT"]),decreasing = FALSE), ]
# mat<-as.data.frame(matrix(unlist(mat), ncol=4))
# colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
# write.table(mat, file=file.path(path, myfile2), row.name=F)
return(mat)
}
print("Putative chlorinated m/z are below")
}else
{
cat(paste("Sorry, NO putative chlorinated compound found \n same player try again \n", sep=""))
mat<-data.frame("No peak", "No peak","No peak", "No peak")
colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
return(mat)
}
}
yguitton/MeHaloCoA documentation built on May 3, 2019, 4:30 p.m.
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#new version 14/07/2014 with check in FUN2 for multiple m/z hits
#change in M1 M2 calculation it was ppm this is confusing pepole ask for 50ppm error and in fact the soft used 60 ppmerr
cldetect<-
function(outdir="",xsAnnotate,plotps=TRUE, deprof=FALSE, Thresh=30, m1=1.0030, m2=1.997, mdiff=0.05, ppmerr=50, val="into", mdiff2=0.001, myfile="halo_list.csv",myfile2="halo_list_short.csv", m1need=FALSE){
if (!class(xsAnnotate) == "xsAnnotate") {
if(class(xsAnnotate)=="list"){
if(length(which(lapply(an,function(x)class(x))=="xsAnnotate"))>=1){
xsAnnotate<-xsAnnotate[[as.vector(which(lapply(an,function(x)class(x))=="xsAnnotate"))]]
}
else{
stop("Parameter object is no xsAnnotate object\n")
}
}
else{
stop("Parameter object is no xsAnnotate object\n")
}
}
#find output directory
path<-outdir
if ((path != "") == FALSE) {
#require(tcltk)
path=tclvalue(tkchooseDirectory(title="Please, select your Results directory"))
}
an=xsAnnotate
#find pspectrum with 2 Da neutral loss for Chlorine, Bromine it is ok
hits <- findNeutralLossSpecs(an, mzdiff=m2, mzabs=mdiff, mzppm=ppmerr)
good<-which(hits==TRUE)
#Find M+2 isotope and its intensity and compare to M+1 and M intensities into can be changed by maxo with val option
funM2<-function(target, massadduct1=m1, massadduct2=m2, mzabs=mdiff, ppmerr=ppmerr, Thresh=Thresh, val=val){
ls_halogenated<-list()
ls_Mlist<-list()
ls_test<-list()
M<-peak[which(peak[,"mz"]==target),val]
M1<-subset(peak,peak[,1]<=(ppm(target,ppmerr,l=TRUE)[1]+massadduct1) & (ppm(target,ppmerr,l=TRUE)[2]+massadduct1)<=peak[,1])#+ 10 ppm error pour le m+2 en limite haute
M2<-subset(peak,peak[,1]<=(ppm(target,ppmerr,l=TRUE)[1]+massadduct2) & (ppm(target,ppmerr,l=TRUE)[2]+massadduct2)<=peak[,1])
#test if several M1 or M2[,"mz"]
if (length(M1[,"mz"])>1){
testvect<-M1[,"mz"]
M1<-M1[which(abs(testvect-target-massadduct1)==min(abs(testvect-target-massadduct1))),]
}
if (length(M2[,"mz"])>1){
testvect<-M2[,"mz"]
M2<-M2[which(abs(testvect-target-massadduct2)==min(abs(testvect-target-massadduct2))),]
}
if (length(M2[,"mz"])!=0){
#Si M+1 et M+2 OK
if ( length(M1[,"mz"])!=0){
test2<-(peak[which(peak[,"mz"]==M2[,"mz"]),val]*100)/peak[which(peak[,"mz"]==target),val][1]
test1<-(peak[which(peak[,"mz"]==M1[,"mz"]),val]*100)/peak[which(peak[,"mz"]==target),val][1]
print(paste("Tests Result for target=",target, "and pcgroup=",good[j]))
print(test2)
print(test1)
#liste des tests
#test1<150 is to avoid peaking M+1 isotopes as a M
if ((test2>=Thresh) && (test1<150) && (test2<600)){
if((M1[,"mz"]-target)[1]>=massadduct1-mzabs){
Halo1<-"OK"
}else
{
Halo1<-"No"
}
if((M2[,"mz"]-target)[1]<=massadduct2+mzabs){
Halo2<-"OK"
}else
{
Halo2<-"No"
}
if(Halo1=="OK" && Halo2=="OK" ){
Halo3<-"OK"
}else
{
Halo3<-"No"
}
if(Halo3=="OK" && test2>90 ){
Br<-"OK"
}else
{
Br<-"No"
}
if(Halo3=="OK" && test2>Thresh ){
Cl<-"OK"
}else
{
Cl<-"No"
}
RT<-round(median(getpspectra(an, grp=as.vector(good)[j])[, "rt"])/60,3)
if (Halo2=="OK"){
cat(j,good[j],RT,M,target,M1[,"mz"][1],M2[,"mz"][1],(M1[,"mz"]-target)[1],(M2[,"mz"]-target)[1],test1[1],test2[1],Halo3,Br,Cl,"\n", file = zz, sep = ",")
ls_halogenated<-good[j]
}
}
}
if(m1need==FALSE){
#Si M+2 OK mais pas M+1 (pas assez intense)
if ( length(M1[,"mz"])==0){
test2<-(peak[which(peak[,"mz"]==M2[,"mz"]),val]*100)/peak[which(peak[,"mz"]==target),val][1]
test1<-"TOO LOW"
#list des test
if ((test2>=Thresh) && (test2<600)){
Halo1<-"M+1 Too Low"
Halo3<-"M+1 Too Low"
Br<-"M+1 Too Low"
Cl<-"M+1 Too Low"
if((M2[,"mz"]-target)[1]<=massadduct2+mzabs){
Halo2<-"OK"
}else
{
Halo2<-"No"
}
RT<-round(median(getpspectra(an, grp=as.vector(good)[j])[, "rt"])/60,3)
if (Halo2=="OK"){
cat(j,good[j],RT,M,target,M1[,"mz"][1],M2[,"mz"][1],(M1[,"mz"]-target)[1],(M2[,"mz"]-target)[1],test1[1],test2[1],Halo3,Br,Cl,"\n", file = zz, sep = ",")
ls_halogenated<-good[j]
}
}
}
}#end if M+1 available
}
if (length(ls_halogenated)!=0){
# reslist<-list("ls_halogenated"=ls_halogenated, "ls_Mlist"=ls_Mlist, "ls_test"=ls_test)
# return(reslist)
return(ls_halogenated)
}
}# end funM2
#j in long = lenght good
zz<-file(file.path(path,myfile), "w")
cat("j","pcgroup","RT","Intensity","M","M1","M2","M1-M","M2-M","M1/M","M2/M","MassDefect filters OK","Br","Cl","\n", file = zz, sep = ",")
ls_good<-list()
if(length(good)!=0){
for (j in 1:length(good)){
ls_target<-list()
peak<-getpspectra(an, good[j])
#remove NaN containing lignes
peak<-peak[complete.cases(peak), ]
if (deprof==TRUE){
options(warn=-1)
if(require(RMassBank)){
peak<-RMassBank::deprofile.scan(peak[,c("mz",val)])
colnames(peak)<-c("mz",val)
options(warn=0)
}else{
stop("Couldn't load RMassBank")
}
}
#ls_target<-peak[sort.list(peak[,"into"], decreasing=TRUE), ][,1]
ls_target<-peak[,1]
ls_halogenated<-lapply(ls_target, function(x)funM2(target=x, massadduct1=m1, massadduct2=m2, mzabs=mdiff, ppmerr=ppmerr, Thresh=Thresh, val=val))
#ls_halogenated
ls_good[[j]]<-peak[which(match(ls_halogenated,good[j])==1),"mz"]
}
}else{
print("No peak")
}
close(zz)
data<-read.table(file.path(path,myfile),header=TRUE, sep=",")
clvect<-unique(data[which(data[,"Cl"]=="OK"),"pcgroup"])
brvect<-unique(data[which(data[,"Br"]=="OK"),"pcgroup"])
ls_good2<-lapply(ls_good,function(x)length(x))
print(ls_good2)
if (plotps==TRUE && length(good[which(ls_good2>=1)])>=1){
#outdirbasicGCplot for outputs just to keep track off the name
outdirbasicGCplot<-file.path(path,paste("EICs_Results_",format(Sys.time(), "%Y_%B_%d_%Hh%M"),sep=""))
#plot pspectra and EICs for good peaks
basicGCplot(outdir=path,xsAnnotate=an,pspecrange= as.vector(good[which(ls_good2>=1)]), check="")
}
if (length(good[which(ls_good2>=1)])>=1){
#if bug change an@xcmsSet@filepaths<-"path to your file"
#Plot IFC
#matrix1 with ls_good list m/z +/- mdiff2
matrix1<-cbind((unlist(ls_good[which(ls_good2>=1)])-mdiff2),(unlist(ls_good[which(ls_good2>=1)])+mdiff2))
mzrange<-matrix(ncol=2, data=matrix1)
print(dim(matrix1))
#1- faire max int de chque pcgroup (peut-etre lors des tests dans fichier final) attention xs = xcmsSet or cldetect accepte seulment le an voir getEICs from CAMERA
peakT<-getPeaklist(an) #peak table
malist<-NULL #start at NULL
for (i in 1:dim(mzrange)[1]){
malist<-c(malist,which(peakT[,"mz"]>mzrange[i,1] & peakT[,"mz"]<mzrange[i,2]))
# print(i) #debug
}
EIC.matrix<-getAllPeakEICs(an,index=rep(1,nrow(an@groupInfo)))
EIC.matrix$EIC[!is.finite(EIC.matrix$EIC)]<-0
#gestion du cas ou is.null(dim(EIC.matrix$EIC[malist,])) ou colSums ne fonctionne pas
if(!is.null(dim(EIC.matrix$EIC[malist,]))){
plot(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC[malist,])+max(colSums(EIC.matrix$EIC))*0.05, type="l", ylim=c(0,max(colSums(EIC.matrix$EIC))),col="Red", main=paste("IFC for \n",basename(an@xcmsSet@filepaths)), xlab="seconds", ylab="Intensity") #IFC
points(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC), type="l", col="grey") # TIC
legend("topright", legend=c("IFC","TIC","Highly Interesting Point"), lty=1, lwd=2, col=c("red","grey","blue"), bty="n")
}else
{
plot(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC), type="l", col="grey", main=paste("IFC for \n",basename(an@xcmsSet@filepaths), "\n Note a problem exists!"), xlab="seconds", ylab="Intensity") #IFC
}
#mat a refaire si plotps=False
rt<-list()
cl<-list()
br<-list()
for(i in 1:length(as.vector(good[which(ls_good2>=1)]))){
rt[i] <- round(median(getpspectra(an, grp=as.vector(good[which(ls_good2>=1)])[i])[, "rt"])/60,3)
cl[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], clvect))
br[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], brvect))
}
mat<-data.frame(cbind(as.numeric(rt),cl,br,lapply(ls_good[which(ls_good2>=1)], FUN=function(x)paste0(round(as.numeric(x),3), collapse="|"))))
colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
mat<-mat[sort.list(unlist(mat[,"RT"]),decreasing = FALSE), ]
#gestion du cas ou length(which(mat[,"Cl OK"]=="TRUE"))<1
if (length(which(mat[,"Cl OK"]=="TRUE"))>=1){
arrows(as.numeric(mat[which(mat[,"Cl OK"]=="TRUE"),"RT"])*60, x1=as.numeric(mat[which(mat[,"Cl OK"]=="TRUE"),"RT"])*60, y0=max(colSums(EIC.matrix$EIC))*0.05, y1=0,col = "blue", lty = "solid", lwd = 2, length = 0.04, angle = 45, code = 1)
}
}else
{
EIC.matrix<-getAllPeakEICs(an,index=rep(1,nrow(an@groupInfo)))
EIC.matrix$EIC[!is.finite(EIC.matrix$EIC)]<-0
plot(x=unlist(EIC.matrix$scantime),y=colSums(EIC.matrix$EIC), type="l", col="grey", main=paste("IFC for \n",basename(an@xcmsSet@filepaths), "\n No Cl or Br"), xlab="seconds", ylab="Intensity") #IFC
}
if (length(good[which(ls_good2>=1)])>=1){
cat("Nan Mais Halo Quoi!,\n Good News, putative chlorinated compound found \n")
cat(paste("Results files are in", outdir))
if (plotps==TRUE){
print(paste("EICs and Mass Spectra are in ",outdirbasicGCplot, sep=""), sep="")
return(mat)
}else{
#return(ls_good[which(ls_good2>=1)])
#Now for RTs for all peaks in the whole an list()
rt<-list()
cl<-list()
br<-list()
for(i in 1:length(as.vector(good[which(ls_good2>=1)]))){
rt[i] <- round(median(getpspectra(an, grp=as.vector(good[which(ls_good2>=1)])[i])[, "rt"])/60,3)
cl[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], clvect))
br[i]<-!is.na(match(as.vector(good[which(ls_good2>=1)])[i], brvect))
}
mat<-data.frame(cbind(as.numeric(rt),cl,br,lapply(ls_good[which(ls_good2>=1)], FUN=function(x)paste0(round(as.numeric(x),3), collapse="|"))))
colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
mat<-mat[sort.list(unlist(mat[,"RT"]),decreasing = FALSE), ]
# mat<-as.data.frame(matrix(unlist(mat), ncol=4))
# colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
# write.table(mat, file=file.path(path, myfile2), row.name=F)
return(mat)
}
print("Putative chlorinated m/z are below")
}else
{
cat(paste("Sorry, NO putative chlorinated compound found \n same player try again \n", sep=""))
mat<-data.frame("No peak", "No peak","No peak", "No peak")
colnames(mat)<-c("RT","Cl OK","Br OK","MZs")
return(mat)
}
}
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