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####### Shimadzu .txt file parsing function
Parse <- function(x){
pos1 <- which(x=="[Header]")
pos2 <- which(x=="[File Information]")
pos3 <- which(x =="[Sample Information]")
pos4 <- which(x=="[MC Peak Table]")
pos5 <- which(x=="[Spectrum Process Table]")
pos6 <- which(x=="[MS Similarity Search Results for Spectrum Process Table]")
pos7 <- which(x== "[MS Chromatogram]")
pos8 <- which(x == "[MS Spectrum]")
####### Header Information
header = vector()
for(i in 1:length(x)){
if(i < pos2){
header <- rbind(header, x[i])
}
}
####### Sample Information
SamInfo <- vector()
for(i in 1:length(x)){
if((i >= pos3) && (i < pos4)){
SamInfo <-rbind(SamInfo, x[i])
}
}
######## MC Peak table
PeakTable <- vector()
for(i in 1:length(x)){
if((i >= pos4) && (i < pos5)){
PeakTable <-rbind(PeakTable, x[i])
PeakTable <- gsub("\t"," ",PeakTable)
}
}
TotalPeak <- PeakTable[2,]
peaks<- PeakTable[-c(1:3),]
peaks <- strsplit(peaks," ",fixed=FALSE)
peaks <- t(sapply(peaks,'[', 1:max(sapply(peaks,length))))
colnames(peaks) <- peaks[1,]
peaks <- peaks[-1,]
peaks <- peaks[,-c(12:13)]
peaks <- data.frame(peaks)
###### MS Spectrum
Spectrum <- vector()
for(i in 1:length(x)){
if((i >= pos5) && (i < pos6)){
Spectrum <-rbind(Spectrum, x[i])
}
}
####### MS Annotation
Annotation <- vector()
for(i in 1:length(x)){
if((i >= pos6) && (i < pos7)){
Annotation <-rbind(Annotation, x[i])
Annotation <- gsub("\t"," ",Annotation)
}
}
###### Gas Chromatogram
Chromatogram <- vector()
for(i in 1:length(x)){
if((i >= pos7) && (i < pos8[1])){
Chromatogram <-rbind(Chromatogram, x[i])
}
}
y <- Chromatogram[-c(1:6),]
y <- gsub("\t"," ",y)
y <- strsplit(y," ",fixed=FALSE)
y <- t(sapply(y,'[',1:max(sapply(y,length))))
colnames(y) <- y[1,]
y <- y[-1,]
y <- data.frame(y)
###### Mass Spectrum
######## Extract all the spectrum into one
MsSpectrum <- vector()
for(i in 1:length(x)){
if(i >= pos8){
MsSpectrum <- rbind(MsSpectrum,x[i])
}
}
###### spliting these spectrum into differnt lists
AllSpectrum <- split(MsSpectrum,cumsum(MsSpectrum[,1] == "[MS Spectrum]"))
zz <- lapply(AllSpectrum,extract) ###### Contains all the formatted spectrum in list form
########### Extracting Data matrix from MC Peak Table and individual Mass Spectrum
########## Peak,RT,Start-RT, End-RT
######### Peak base m/z extract and sum of relative intensity (TIC)
data <- peaks[,1:4]
data <- na.omit(data)
total <- lapply(zz,FinalTable)
total <- t(sapply(total,'[',1:max(sapply(total,length))))
tt <- cbind(data,total)
tt <- as.matrix(tt)
colnames(tt) <- c("Peaks","RT","StartRT","EndRT","MSPeaks","MZ","TIC")
tt <- gsub("m/z","",tt)
tt <- gsub("\\(.*)","",tt)
tt <- data.frame(tt)
new("parse.Shimadzu",McPeakTable=peaks,Annotation=Annotation,GasChromatogram=y,MassSpectrum = zz,FinalTable=tt)
}
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