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## referencePeaks
## calculate reference peaks (a wrapper around filterPeaks and binPeaks)
##
## params:
## l: list of MassPeaks objects
## method: character, grouper to used (strict: don't allow multiple peaks of
## the same sample in the same bin, relaxed: allow them)
## minFrequency: double, minimal frequency of a peak to be not removed
## tolerance: double, maximal deviation of a peak position to be
## considered as same peak
##
## returns:
## a new MassPeaks object
##
referencePeaks <- function(l, method=c("strict", "relaxed"), minFrequency=0.9,
tolerance=0.002) {
.stopIfNotIsMassPeaksList(l)
method <- match.arg(method)
## find reference peaks by binning and filtering
referencePeaks <- filterPeaks(binPeaks(l, method=method,
tolerance=tolerance),
minFrequency=minFrequency)
m <- .as.binary.matrix(.as.matrix.MassObjectList(referencePeaks))
## set peak intensity to number of occurrence
intensity <- unname(colMeans(m))
createMassPeaks(mass=attr(m, "mass"), intensity=intensity)
}
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