Hi,
first I have to say that I just started using R, I tried to find some answers in this
forum but did not succeed.
I am looking for a documentation of the different methods for feature detection
and their parameters.
Further I do not understand all columns in the peaks table after peak detection:
mz, mzmin, mzmax, rt, rtmin, rtmax and sn are self explaining. But what do
into, intf, maxo, maxf, i and sample mean ?
Regards, Uwe
Hi,
R has some extensive documentation in form of manual pages,
they take a bit to get used to, but are well structured.
Check e.g. help("findPeaks.matchedFilter") or help("findPeaks.centWave").
Also, check the papers for more on the algorithm:
Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and
Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite
profiling using nonlinear peak alignment, matching and
identification, Analytical Chemistry, 78:779-787 (2006)
Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly
sensitive feature detection for high resolution LC/MS BMC
Bioinformatics, 9:504 (2008)
Hope that helped,
Yours,
Steffen