Description Usage Arguments Details Value Author(s) Examples

Compute three quality parameters for a set of spectra.

1 | ```
quality(Ma, peakinfofile, cutoff)
``` |

`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 |

`cutoff` |
The point in m/z below which spectra are cutoff. |

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.

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

Xiaochun Li

1 2 |

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