MSImagingInfo-class {Cardinal} | R Documentation

## MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion

### Description

The `MSImagingInfo` class is designed to contain metadata for reading/writing Cardinal objects from/to imzML files.

### Methods

`length(object)`:

  The number of scans (i.e., the number of mass spectra).

`scans(object)`:

  Access the scan list metadata for writing to imzML.

`mzData(object)`:

  Access the m/z array list metadata for writing to imzML.

`intensityData(object)`:

  Access the intensity array list metadata for writing to imzML.

`isCentroided(object)`:

  Check whether the mass spectra are centroided.

`normalization(object), normalization(object) <- value`:

  Accessor and setter function for the `normalization`.

`smoothing(object), smoothing(object) <- value`:

  Accessor and setter function for the `smoothing`.

`baselineReduction(object), baselineReduction(object) <- value`:

  Accessor and setter function for the `baselineReduction`.

`peakPicking(object), peakPicking(object) <- value`:

  Accessor and setter function for the `peakPicking`.

`spectrumRepresentation(object), spectrumRepresentation(object) <- value`:

  Accessor and setter function for the `spectrumRepresentation`.

`matrixApplication(object)`:

  Accessor function for `matrixApplication`.

`pixelSize(object)`:

  Accessor function for `pixelSize`.

`instrumentModel(object)`:

  Accessor function for `instrumentModel`.

`instrumentVendor(object)`:

  Accessor function for `instrumentVendor`.

`massAnalyzerType(object)`:

  Accessor function for `massAnalyzerType`.

`ionizationType(object)`:

  Accessor function for `ionizationType`.

`scanPolarity(object)`:

  Accessor function for `scanPolarity`.

`scanType(object)`:

  Accessor function for `scanType`.

`scanPattern(object)`:

  Accessor function for `scanPattern`.

`scanDirection(object)`:

  Accessor function for `scanDirection`.

`lineScanDirection(object)`:

  Accessor function for `lineScanDirection`.

### Author(s)

Kylie A. Bemis

### References

Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprevote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Rompp A (2012) imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data. Journal of Proteomics 75 (16):5106-5110. doi:10.1016/j.jprot.2012.07.026

### See Also

`MIAxE`, `MIAPE-Imaging`

### Examples

    mz <- mz(from=200, to=220, by=400)
    coord <- expand.grid(x=1:3, y=1:3)
    data <- matrix(runif(length(mz) * nrow(coord)),
        nrow=length(mz), ncol=nrow(coord))

    x <- MSImagingExperiment(
        imageData=ImageArrayList(data),
        featureData=MassDataFrame(mz=mz),
        pixelData=PositionDataFrame(coord=coord))

    msiInfo(x)

[Package Cardinal version 2.12.0 Index]