getPeaks: Peak Detection
In PROcess: Ciphergen SELDI-TOF Processing

Description Usage Arguments Details Author(s) See Also Examples

For given threshold criteria, find peaks.

1 2	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

rmBaseline

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

Loading required package: Icens
Loading required package: survival

Attaching package: 'PROcess'

The following object is masked from 'package:stats':

    sigma


renorm> example(rmBaseline)

rmBsln> testdir <- system.file("Test", package = "PROcess")

rmBsln> testM <- rmBaseline(testdir)

renorm> rtM <- renorm(testM, cutoff=1500)
Warning messages:
1: In min(y) : no non-missing arguments to min; returning Inf
2: In min(y) : no non-missing arguments to min; returning Inf