# [R] SLLOOOWWW function ...

Johannes Graumann johannes_graumann at web.de
Tue Jul 17 13:32:07 CEST 2007

```Does anybody have any insight into how to make this faster?
I suspect, that the rounding going on may be an issue, as is the stepping
through data frame rows using integers ...

If you have the patience to teach a noob, he will highly appreciate it ;0)

Joh

digit <- 4
for (minute in seq(from=25,to=lrange)){
# Extract all data associtaed with the current time (minute)
frame <- subset(mylist,mylist[["Time"]] == minute)
# Sort by Intensity
frame <- frame[order(frame[["Intensity"]],decreasing = TRUE),]
# Establish output frame using the most intense candidate
newframe <- frame[1,]
# Establish overlap-checking vector using the most intense candidate
lowppm <- round(newframe[1,][["Mass"]]-newframe[1,
[["Mass"]]/1E6*ppmrange,digits=digit)
highppm <- round(newframe[1,][["Mass"]]+newframe[1,
[["Mass"]]/1E6*ppmrange,digits=digit)
presence <- seq(from=lowppm,to=highppm,by=10^(-digit))
# Walk through the entire original frame and check whether peaks are
overlap-free ... do so until max of 2000 entries
for (int in seq(from=2,to=nrow(frame))) {
if(nrow(newframe) < 2000) {
lowppm <- round(frame[int,][["Mass"]]-frame[int,
[["Mass"]]/1E6*ppmrange,digits=digit)
highppm <- round(frame[int,][["Mass"]]+frame[int,
[["Mass"]]/1E6*ppmrange,digits=digit)
windowrange <- seq(from=lowppm,to=highppm,by=10^(-digit))
if (sum(round(windowrange,digits=digit) %in%
round(presence,digits=digit)) < 1) {
newframe <- rbind(newframe,frame[int,])
presence <- c(presence,windowrange)
}
} else {
break()
}
}

```