pk2bmkr: Find Biomarkers.
In PROcess: Ciphergen SELDI-TOF Processing

Description Usage Arguments Value Author(s) References See Also Examples

Align peaks of spectra in ‘peakinfofile’ and find biomarkers by a procedure described in Gentleman and Geyer (1994).

1	pk2bmkr(peakinfofile, bseoffM, bmkfile, eps = 0.003, binary = F,p.fltr = 0.1)

`peakinfofile`	a ‘.csv’ file in the same format as Ciphergen's peakinfo file with 5 columns data, Spectrum.Tag, Spectrum., Peak., Intensity and Substance.Mass.
`bseoffM`	a matrix holding the baseline-substracted spectra, with row-names as the m/z values and column-names as the spectrum names.
`bmkfile`	a ‘.csv’ file in the same format as Ciphergen's biomarker file, with spectra (samples) as columns, and biomarkers as rows.
`eps`	expected experimental variation in the m/z values.
`binary`	output intensity or binary peak presence/absence signals.
`p.fltr`	a number between 0 and 1. If a proto-biomarker is identified as peak in > p.fltr x 100 percent of spectra, it's kept in 'bmkfile'.

A dataframe with spectra as rows and biomarkers as columns. Spectrum labels and biomarker positions may be in the names of the dataframe.

Xiaochun Li

Gentleman, R. and Geyer, C.J. (1994). Maximum likelihood for interval censored data: Consistency and computation. Biometrika, 81:618–623.

rmBaseline,getPeaks

example(getPeaks)
bmkfile <- paste(tempdir(),"testbiomarker.csv",sep="/")
testBio <- pk2bmkr(peakfile, rtM, bmkfile)

## plot biomarker intensities of the 2 spectra

mzs <- as.numeric(rownames(rtM))
matplot(mzs, rtM, type="l", xlim=c(1000, 10000))

bks <- getMzs(testBio)
abline(v=bks, col="green")