getPeaks {PROcess} | R Documentation |
For given threshold criteria, find peaks.
getPeaks(bseoffM, peakinfofile,SoN = 2,span = 81,sm.span=11, zerothrsh=2, area.w = 0.003, ratio = 0.2)
bseoffM |
a matrix holding the baseline-substracted spectra, with row-names as the m/z values and column-names as the spectrum names. |
peakinfofile |
a `.csv' file in the same format as Ciphergen's peak info file, with 5 columns data. More details later. |
SoN |
see isPeak(). |
span |
see isPeak(). |
sm.span |
see isPeak(). |
zerothrsh |
ignore peaks whose intensity values are below zerothrsh. |
area.w |
see isPeak(). |
ratio |
see isPeak(). |
For given threshold criteria, detect peaks and write the following columns of information into 'peakinfofile', spectrum name (Spectrum.Tag), spectrum sequential number (Spectrum.), peak sequential number within a spectrum (Peak.), relative intensity (Intensity) and the m/z value where the relative intensity occurs (Substance.Mass).
Xiaochun Li
example(renorm) peakfile <- paste(tempdir(),"testpeakinfo.csv", sep="/") getPeaks(rtM, peakfile)