pk2bmkr: Find Biomarkers.

Description

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

Usage

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

Arguments

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'.

Value

columns. Spectrum labels and biomarker positions may be in the names of the dataframe.

References

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

Examples

Run this code

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")