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.

peakData(object):

Access the intensity array list metadata for writing to imzML (identical to imageData(object)).

imageData(object):

Access the intensity array list metadata for writing to imzML (identical to peakData(object)).

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 peakPicking.

matrixApplication(object), matrixApplication(object) <- value:

Accessor and setter function for matrixApplication.

pixelSize(object), pixelSize(object) <- value:

Accessor and setter function for pixelSize.

instrumentModel(object), instrumentModel(object) <- value:

Accessor and setter function for instrumentModel.

instrumentVendor(object), instrumentVendor(object) <- value:

Accessor and setter function for instrumentVendor.

massAnalyzerType(object), massAnalyzerType(object) <- value:

Accessor and setter function for massAnalyzerType.

ionizationType(object), ionizationType(object) <- value:

Accessor and setter function for ionizationType.

scanPolarity(object), scanPolarity(object) <- value:

Accessor and setter function for scanPolarity.

scanType(object), scanType(object) <- value:

Accessor and setter function for scanType.

scanPattern(object), scanPattern(object) <- value:

Accessor and setter function for scanPattern.

scanDirection(object), scanDirection(object) <- value:

Accessor and setter function for scanDirection.

lineScanDirection(object), lineScanDirection(object) <- value:

Accessor and setter 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

data <- matrix(1:9^2, nrow=9, ncol=9)
mz <- seq(from=100, to=105, length.out=9)
coord <- expand.grid(x=1:3, y=1:3)

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

msiInfo(x)