Slots
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.
Extends
Class MIAxE, directly,
Class Versioned, by class "MIAxE", distance 2.Creating Objects
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.Methods
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.