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lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
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Peakpicking for Chromatogram instances #544

Closed SumedhSankhe closed 3 years ago

SumedhSankhe commented 3 years ago

Hi Laurent,

I hope you are doing well, I am trying to automate the peak picking process and the data that I have is only chromatograms. I was able to read the chromatograms in via readSRMData() but I am not sure if MSnbase has peak picking abilities for chromatogram instances. Is there a suggested workflow that might be useful for this use case?

Sumedh

jorainer commented 3 years ago

The chromatographic peak detection functionality is available in the xcms package. If you have a MChromatograms object from MSnbase you can simply use the findChromPeaks method on that with e.g. a CentWaveParam object to select centWave-based peak detection and pass the parameters to that algorithm along.

Maybe first have a look at the xcms vignette to get a first overview or see directly the help of the method on MChromatograms here.

SumedhSankhe commented 3 years ago

Thanks Johannes! For pointing me to xcms, I had stumbled across is a few days back will definitely give it a more thorough look !