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 1.3.2

Index]