findPeaks.centWave-methods {xcms} | R Documentation |
Peak density and wavelet based feature detection for high resolution LC/MS data in centroid mode
object |
xcmsSet object |
ppm |
maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million) |
peakwidth |
Chromatographic peak width, given as range (min,max) in seconds |
snthresh |
signal to noise ratio cutoff, definition see below. |
prefilter |
prefilter=c(k,I) . Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I . |
integrate |
Integration method. If =1 peak limits are found through descent on the mexican hat filtered data, if =2 the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.
|
mzdiff |
minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap |
fitgauss |
logical, if TRUE a Gaussian is fitted to each peak |
scanrange |
scan range to process |
sleep |
number of seconds to pause between plotting peak finding cycles |
verbose.columns |
logical, if TRUE additional peak meta data columns are returned |
This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode. In the first phase of the method mass traces (characterised as regions with less than ppm
m/z deviation in consecutive scans) in the LC/MS map are located.
In the second phase these mass traces are further analysed.
Continuous wavelet transform (CWT) is used to locate chromatographic peaks on different scales.
A matrix with columns:
mz |
weighted (by intensity) mean of peak m/z across scans |
mzmin |
m/z peak minimum |
mzmax |
m/z peak maximum |
rt |
retention time of peak midpoint |
rtmin |
leading edge of peak retention time |
rtmax |
trailing edge of peak retention time |
into |
integrated peak intensity |
intb |
baseline corrected integrated peak intensity |
maxo |
maximum peak intensity |
sn |
Signal/Noise ratio, defined as (maxo - baseline)/sd , where maxo is the maximum peak intensity, baseline the estimated baseline value and sd the standard deviation of local chromatographic noise.
|
egauss |
RMSE of Gaussian fit |
|
if verbose.columns is TRUE additionally :
|
mu |
Gaussian parameter mu |
sigma |
Gaussian parameter sigma |
h |
Gaussian parameter h |
f |
Region number of m/z ROI where the peak was localised |
dppm |
m/z deviation of mass trace across scans in ppm |
scale |
Scale on which the peak was localised |
scpos |
Peak position found by wavelet analysis |
scmin |
Left peak limit found by wavelet analysis (scan number) |
scmax |
Right peak limit found by wavelet analysis (scan number) |
findPeaks.centWave(object, ppm=25, peakwidth=c(20,50), snthresh=10,
prefilter=c(3,100), integrate=1, mzdiff=-0.001, fitgauss=FALSE,
scanrange= numeric(), sleep=0, verbose.columns=FALSE)
Ralf Tautenhahn, rtautenh@ipb-halle.de
findPeaks-methods
xcmsRaw-class