MIAPE-Imaging-class {Cardinal} | R Documentation

## MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

### Description

The Minimum Information About a Proteomics Experiment for MS Imaging. The current implementation is based on the imzML specification.

### 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.

### 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`, `MSImageSet`

### Examples

    showClass("MIAPE-Imaging")

[Package Cardinal version 2.2.6 Index]