Do i need to specify polarization for xcmsRaw object ? If yes - how ? For example, xcmsSet class have parameter "polarity", but xcmsRaw - no. At the end of the end, i just want to reproduce with R results of Maven peak peaking procedure... and now my data and data from Maven are different.
So, how i can specify intensity threshold to 1000, for example ?
It is very interesting. So, xcmsSet it is just a set/collection of xsmsRaw objects, which pass arguments from it constructor to constructors of it's inner xsmsRaw classes/objects ? And then automatically run findPeaks procedure width default peaker findPeaks.matchedFilter. Ok, now i'm understand why constructions like this is works fine:
findPeaks.centWave-methods package:xcms R Documentation
Feature detection for high resolution LC/MS data
Description:
Peak density and wavelet based feature detection for high resolution LC/MS data in centroid mode
Arguments:
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’.
mzCenterFun: Function to calculate the m/z center of the feature: ‘wMean’ intensity weighted mean of the feature m/z values, ‘mean’ mean of the feature m/z values, ‘apex’ use m/z value at peak apex, ‘wMeanApex3’ intensity weighted mean of the m/z value at peak apex and the m/z value left and right of it, ‘meanApex3’ mean of the m/z value at peak apex and the m/z value left and right of it.
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
noise: optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity < ‘noise’ are omitted from ROI detection
sleep: number of seconds to pause between plotting peak finding cycles
verbose.columns: logical, if TRUE additional peak meta data columns are returned
Details:
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.
Value:
A matrix with columns:
mz: weighted (by intensity) mean of peak m/z across scans
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)
zeleniy@zeleniy-HP-Pro-3400:~/workspace/mass/peaks$ Rscript xcms.r Loading required package: methods Error in function (classes, fdef, mtable) : unable to find an inherited method for function "findPeaks.centWave", for signature "NULL" Calls: findPeaks.centWave -> <Anonymous> Execution halted
zeleniy@zeleniy-HP-Pro-3400:~/workspace/mass/peaks$ Rscript xcms.r Loading required package: methods ecoli1_600_pos_1: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "findPeaks", for signature "NULL" Calls: xcmsSet -> findPeaks -> <Anonymous> Execution halted
Loading required package: methods ecoli1_600_pos_1: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "findPeaks", for signature "NULL" Calls: xcmsSet -> findPeaks -> <Anonymous> Execution halted