Description Arguments Details Value Methods See Also
A number of peak pickers exist in XCMS. findPeaks
is the generic method.
object |
|
method |
Method to use for peak detection. See details. |
... |
Optional arguments to be passed along |
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
.
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.
findPeaks(object, ...)
findPeaks.matchedFilter
findPeaks.centWave
findPeaks.addPredictedIsotopeFeatures
findPeaks.centWaveWithPredictedIsotopeROIs
xcmsRaw-class
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