Johannes Rainer

You should not just copy-paste the lines from my script. I am calling R and then the `render` function to process the *.Rmd* file (which is a file containing R...

Hi @cbroeckl , unfortunately I don't have any *real* data or benchmarks for all your questions. But I can provide some general remarks and suggestions (which base mainly on experience...

Some notes on evaluating memory consumption in R, I usually use `peakRAM()` from the `peakRAM` package that reports the max memory usage of a call. Regarding your files, it could...

Hi Fang, assuming you are reading the raw data with the `mode = "onDisk"`, you can save the `OnDiskMSnExp` after the `readMSData` call, but very importantly, you should ensure to...

Is there any specific reasons you want to close the R session and re-open it? Usually you don't need to do that. I would only save the data after some...

The `compareChromatograms` function has different parameters than the `correlate` function, thus, you can not use it in exactly the same way. To get the same results you need to call:...

You are on the right track @rromoli . The `readSRMData` actually returns a `Chromatograms` object (the same type of object you would get by calling `chromatogram` on an `MSnExp`/`OnDiskMSnExp` object...

Actually, you're the first user of this functionality! I've never analyzed MRM data (or had any MRM files available for testing). The FTXX is just an arbitrary feature identifier. The...

Thanks for the data! To get the information about the transision for the individual features you can do the following (variable `peaks` is your `Chromatograms` object after peak detection and...

There's nothing specifically for MRM data, except that you can read the data as a `MChromatograms` object and then perform chromatographic peak detection in each chromatogram (using the `findChromPeaks` function),...