Data processing script to get maximum m/z ion intensity pair from Agilent recursive analysis

max intensity mass to charge pair.r

#directory (file path) where the file is 
#note make sure all \ are changed to \\ or /
dir<-"ZZZ"
setwd(dir) # change directory

#name of file, should be .csv
file.name<-"XXX.csv"

#load data into R this assumes there is a header
input<-read.csv(file.name, header = TRUE) 

#now process each string and extract highest intensity pair
# if seems to take to long tell me and I will write the code to do this in parallel
#define function to do the work
get.max.pair<-function(input, save=TRUE){
  #input is imported list which is assumed to be a data.frame
	# if save = TRUE the results will be saved as "max.pair.csv" in the working directory
	input<-as.matrix(input)
	out<-do.call("rbind",lapply(1:nrow(input), function(i)
		{
			obj<-gsub(")","",unlist(gsub("(","",unlist(strsplit(input[i,],split=")(",fixed = TRUE)), fixed=TRUE)),fixed=TRUE)
			obj2<-matrix(as.numeric(unlist(strsplit(as.character(obj),"\\,"))),ncol=2, byrow=TRUE)
			obj2[which.max(obj2[,2]),]
		}))
		colnames (out)<-c("max intensity m/z","intensity")
	if (save == TRUE){	
		write.csv(as.data.frame(out),file="max.pair.csv")	
	} else {
			return(out)
			}
}

#now run the function on your uploaded data
get.max.pair(input, save=TRUE)