class.MIAME: Class for Storing Microarray Experiment Information

In Biobase: Biobase: Base functions for Bioconductor

Description

Class MIAME covers MIAME entries that are not covered by other classes in Bioconductor. Namely, experimental design, samples, hybridizations, normalization controls, and pre-processing information. The MIAME class is derived from MIAxE.

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

samples:

Object of class list containing information about the samples

hybridizations:

Object of class list containing information about the hybridizations

normControls:

Object of class list containing information about the controls such as house keeping genes

preprocessing:

Object of class list containing information about the pre-processing steps used on the raw data from this experiment

pubMedIds:

Object of class character listing strings of PubMed identifiers of papers relevant to the dataset

other:

Object of class list containing other information for which none of the above slots does not applies

Methods

Constructor methods:

MIAME():

MIAME(name = "", lab = "", contact = "", title = "", abstract = "", url = "", pubMedIds = "" , samples = "", hybridizations = list(), normControls = list(), preprocessing = list(), other = list()): Creates a new MIAME object with slots as defined above.

Class-specific methods:

abstract(MIAME):

An accessor function for abstract.

combine(MIAME,MIAME):

Combine two objects of MIAME-class, issuing warnings when ambiguities encountered.

expinfo(MIAME):

An accessor function for name, lab, contact, title, and url.

hybridizations(MIAME):

An accessor function for hybridizations.

normControls(MIAME):

An accessor function for normControls.

notes(MIAME), notes(MIAME) <- value:

Accessor functions for other. notes(MIAME) <- character appends character to notes; use notes(MIAME) <- list to replace the notes entirely.

otherInfo(MIAME):

An accessor function for other.

preproc(MIAME):

An accessor function for preprocessing.

pubMedIds(MIAME), pubMedIds(MIAME) <- value:

Accessor function for pubMedIds.

samples(MIAME):

An accessor function for samples.

Standard generic methods:

updateObject(object, ..., verbose=FALSE)

Update instance to current version, if necessary. See updateObject

isCurrent(object)

Determine whether version of object is current. See isCurrent

isVersioned(object)

Determine whether object contains a 'version' string describing its structure . See isVersioned

show(MIAME):

Renders information about the MIAME information

Author(s)

Rafael A. Irizarry

References

http://www.mged.org/Workgroups/MIAME/miame_1.1.html

See Also

class:characterORMIAME, read.MIAME

Biobase documentation built on Nov. 8, 2020, 6:52 p.m.