MIAPE-Imaging-class {Cardinal} | R Documentation |
The Minimum Information About a Proteomics Experiment for MS Imaging. The current implementation is based on the imzML specification.
name
:Object of class character
containing the experimenter name
lab
:Object of class character
containing the laboratory where the experiment was conducted.
contact
:Object of class character
containing contact information for lab and/or experimenter.
title
:Object of class character
containing a single-sentence experiment title.
abstract
:Object of class character
containing an abstract describing the experiment.
url
:Object of class character
containing a URL for the experiment.
pubMedIds
:Object of class character
listing strings of PubMed identifiers of papers relevant to the dataset.
samples
:Object of class list
containing information about the samples.
preprocessing
:Object of class list
containing information about the pre-processing steps used on the raw data from this experiment.
other
:Object of class list
containing other information for which none of the above slots does not applies.
specimenOrigin
:Object of class character
describing the specimen origin (institution, ...).
specimenType
:Object of class character
describing the specimen type (species, organ, ...).
stainingMethod
:Object of class character
describing the staining method, if any, applied to the sample (H&E, ...).
tissueThickness
:Object of class numeric
giving the tissue thickness in micrometers (um).
tissueWash
:Object of class character
describing the wash method (spray, dipping, ...).
embeddingMethod
:Object of class character
describing the embedding method (if any); this could be paraffin, ...
inSituChemistry
:Object of class character
describing any on-sample chemistry (tryptic digest, ...)
matrixApplication
:Object of class character
describing how the matrix was applied, if applicable
pixelSize
:Object of class numeric
describing the size of the pixels in micrometers (um).
instrumentModel
:Object of class character
indicating the instrument model used to generate the data.
instrumentVendor
:Object of class character
indicating the mass spectrometer vendor.
massAnalyzerType
:Object of class character
describing the mass analyzer type (LTQ, TOF, ...).
ionizationType
:Object of class character
describing the ionization type (MALDI, DESI, ...).
scanPolarity
:Object of class character
describing the polarity (negative or positive).
softwareName
:Object of class character
with the control and/or analysis software name.
softwareVersion
:Object of class character
with the version of the control and/or analysis software.
scanType
:Object of class character
describing the scan type. This must be either 'horizontal line scan' or 'vertical line scan'. See the imzML specifications for more details.
scanPattern
:Object of class character
describing the scan type. This must be one of 'flyback', 'meandering', or 'random access'. See the imzML specifications for more details.
scanDirection
:Object of class character
describing the scan type. This must be one of 'bottom up', 'left right', 'right left', or 'top down'. See the imzML specifications for more details.
lineScanDirection
:Object of class character
describing the scan type. This must be one of 'linescan bottom up', 'linescan left right', 'linescan right left', or 'linescan top down'. See the imzML specifications for more details.
imageShape
:Object of class character
describing the image shape (rectangular, free form, ...). See the imzML specifications for more details.
Class MIAxE
, directly,
Class Versioned
, by class "MIAxE", distance 2.
MIAPE-Imaging
instances can be created through new("MIAPE-Imaging")
. In general, instances should not be created by the user, but are automatically generated when reading an external file to create an MSImageSet
object, and then modified through the accessor and setter methods if necessary.
Class-specific methods:
msiInfo
:Displays 'MIAPE-Imaging' information.
abstract
:An accessor function for abstract
.
expinfo
:An accessor function for name
, lab
, contact
, title
, and url
.
notes(object), notes(object) <- value
:Accessor functions for other
. notes(object) <- character
appends character to notes; use notes(object) <- list
to replace the notes entirely.
otherInfo
:An accessor function for other
.
preproc
:An accessor function for preprocessing
.
pubMedIds(object), pubMedIds(object) <- value
:Accessor function for pubMedIds
.
samples
:An accessor function for samples
.
specimenOrigin(object), specimenOrigin(object) <- value
:Accessor and setter function for specimenOrigin
.
specimenType(object), specimenType(object) <- value
:Accessor and setter function for specimenType
.
stainingMethod(object), stainingMethod(object) <- value
:Accessor and setter function for stainingMethod
.
tissueThickness(object), tissueThickness(object) <- value
:Accessor and setter function for tissueThickness
.
tissueWash(object), tissueWash(object) <- value
:Accessor and setter function for tissueWash
.
embeddingMethod(object), embeddingMethod(object) <- value
:Accessor and setter function for embeddingMethod
.
inSituChemistry(object), inSituChemistry(object) <- value
:Accessor and setter function for inSituChemistry
.
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
.
softwareName(object), softwareName(object) <- value
:Accessor and setter function for softwareName
.
softwareVersion(object), softwareVersion(object) <- value
:Accessor and setter function for softwareVersion
.
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
.
imageShape(object), imageShape(object) <- value
:Accessor and setter function for imageShape
.
Standard generic methods:
show
:Displays object content.
combine(x, y, ...)
:Combine two or more MIAPE-Imaging
objects.
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
showClass("MIAPE-Imaging")