proFIAset-class {proFIA} | R Documentation

## An S4 class to represent an FIA experiments.

### Description

The S4 class also includes all the informations about processing, and the detected signals are stored.

### Usage

    ## S4 method for signature 'proFIAset'
    phenoClasses(object)

    ## S4 method for signature 'proFIAset'
    dataMatrix(object)

    ## S4 method for signature 'proFIAset'
    groupMatrix(object)

    ## S4 method for signature 'proFIAset'
    peaks(object)

    ## S4 method for signature 'proFIAset'
    injectionPeaks(object)

### Arguments

`object` | A proFIAset object.

### Methods (by generic)

- `phenoClasses`: Extract the classes and the paths of the samples.

- `dataMatrix`: Extract the dataMatrix containg variables as rows and samples as columns

- `groupMatrix`: Extract the matrix of group, see `exportPeakTable` for better output.

- `peaks`: Extract all the signals detected in individual samples.

- `injectionPeaks`: Extract all the regressed injection peaks.

### Slots

`peaks`

  A matrix containg all the peaks which have been detected in each individual files.

  - mzmin the minimum value of the mass traces in the m/z dimension.

  - mzmax the maximum value of the mass traces in the m/z dimension.

  - scanMin the first scan on which the signal is detected.

  - scanMax the last scan on which the signal is detected.

  - areaIntensity the integrated area of the signal.

  - maxIntensity the maximum intensity of the signal.

  - solventIntensity the intensity of the solvent, 0 means that no significant solvent was detected.

  - corSampPeak An idicator of matrix effect, if it's close to 1, the compound does not suffer from heavy matrix effect, if it is inferior to 0.5, the compound suffer from heavy matrix effect.

  - signalOverSolventRatio The ratio of the signal max intensity on the oslvent max intensity.

`group`

  A matrix containing the information on the groups done between all the acquisitions.

  - mzMed the median value of group in the m/z dimension.

  - mzMin the minimum value of the group in the m/z dimension.

  - mzMax the maximum value of the group in the m/z dimension.

  - scanMin the first scan on which the signal is detected.

  - scanMax the last scan on which the signal is detected.

  - nPeaks The number of peaks grouped in a group.

  - meanSolvent The mean of solvent in the acquisition.

  - pvalueMedian The median p-value of the group.

  - corMean The mean of the matrix effect indicator.

  - signalOverSolventMean The mean of ratio of the signal max intensity on the oslvent max intensity.

  - corSd The standard deviation of the matrix effect indicator.

  - timeShifted Is the peak shifted compared to the injection peak.

`groupidx`

  The row of the peaks corresponding to each group in `peaks`.

`step`

  The step of processing of the experiment.

`path`

  The path of the experiment.

`classes`

  A table with two columns, "rname" the absolute path of a file, and "group" the class to which the file belong.

`dataMatrix`

  A matrix variables x experiments suitable for statistical analysis.

`noiseEstimation`

  A model of noise as estimated by estimateNoiseMS

`injectionPeaks`

  A list of the injection peak which have been detected for each experiment.

`injectionScan`

  A numeric vector giving the scan of injection of sample.

[Package proFIA version 1.6.0 Index]