pk2bmkr {PROcess} | R Documentation

## 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

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

### Author(s)

Xiaochun Li

### References

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

### See Also

`rmBaseline`,`getPeaks`

### Examples

    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")

[Package PROcess version 1.60.0 Index]