quality {PROcess} | R Documentation

## Quality Check on a Set of Spectra

### Description

Compute three quality parameters for a set of spectra.

### Usage

    quality(Ma, peakinfofile, cutoff)

### Arguments

`Ma` | a Matrix where the baseline-subtracted spectra are stored column wise.
`peakinfofile` | a ‘.csv’ file in the same format as Ciphergen's peak info file, with 5 columns data. See Details of `getPeaks`.
`cutoff` | The point in m/z below which spectra are cutoff.

### Details

The quality parameters are computed a la fashion de Mani. 1. Estimate noise by moving average with a 5 point window. 2. Estimate the noise envelop by 3 times the standard deviation of noise in a 251 point moving window. 3. Compute the area under the baseline-subtracted curve, area0. 4. Compute the area after subtracting the noise envelop from the baseline-subtracted curve, area1. 5. Parameter 'Quality' is defined as area1/area0. 6. Parameter 'Retain' is defined as the number of points with height above 5 times the noise envelop over total number of points in the spectrum. 7. Detect peaks in each spectrum by `getPeaks` or Ciphergen software. 8. Parameter 'peak' is defined as the number of peaks in a spectrum divided by the mean number of peaks across spectra.

A spectrum is considered to be of poor quality if Quality<0.4, Retain<0.1 and peak<0.5 simultaneously.

### Value

A matrix with three named columns, 'Quality','Retain' and 'peak', with spectrum file names as row names.

### Author(s)

Xiaochun Li

### Examples

    example(getPeaks)
    qualRes <- quality(testM, peakfile, cutoff=1500)

[Package PROcess version 1.66.0 Index]