MSImagingInfo-class {Cardinal} | R Documentation |
The MSImagingInfo
class is designed to contain metadata for reading/writing Cardinal objects from/to imzML files.
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
.
Kylie A. Bemis
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
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)