Feature detection for GC/MS and LC/MS Data - methods
findPeaks-methods.RdA number of peak pickers exist in XCMS. findPeaks
is the generic method.
Arguments
- object
xcmsRaw-classobject- method
Method to use for peak detection. See details.
- ...
Optional arguments to be passed along
Details
Different algorithms can be used by specifying them with the
method argument. For example to use the matched filter
approach described by Smith et al (2006) one would use:
findPeaks(object, method="matchedFilter"). This is also
the default.
Further arguments given by ... are
passed through to the function implementing
the method.
A character vector of nicknames for the
algorithms available is returned by
getOption("BioC")$xcms$findPeaks.methods.
If the nickname of a method is called "centWave",
the help page for that specific method can
be accessed with ?findPeaks.centWave.
Value
A matrix with columns:
- mz
weighted (by intensity) mean of peak m/z across scans
- mzmin
m/z of minimum step
- mzmax
m/z of maximum step
- rt
retention time of peak midpoint
- rtmin
leading edge of peak retention time
- rtmax
trailing edge of peak retention time
- into
integrated area of original (raw) peak
- maxo
maximum intensity of original (raw) peak
and additional columns depending on the choosen method.