PROcess (version 1.48.0)

getPeaks: Peak Detection

Description

For given threshold criteria, find peaks.

Usage

getPeaks(bseoffM, peakinfofile,SoN = 2,span = 81,sm.span=11, 
zerothrsh=2, area.w = 0.003, ratio = 0.2)

Arguments

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().

Details

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).

See Also

rmBaseline

Examples

example(renorm)
peakfile <- paste(tempdir(),"testpeakinfo.csv", sep="/")
getPeaks(rtM, peakfile)