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)