MIAME {Biobase} | R Documentation |
Class for Storing Microarray Experiment Information
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 namelab
:Object of class
character
containing the laboratory where the experiment was conductedcontact
:Object of class
character
containing contact information for lab and/or experimentertitle
:Object of class
character
containing a single-sentence experiment titleabstract
:Object of class
character
containing an abstract describing the experimenturl
:Object of class
character
containing a URL for the experimentsamples
:Object of class
list
containing information about the sampleshybridizations
:Object of class
list
containing information about the hybridizationsnormControls
:Object of class
list
containing information about the controls such as house keeping genespreprocessing
:Object of class
list
containing information about the pre-processing steps used on the raw data from this experimentpubMedIds
:Object of class
character
listing strings of PubMed identifiers of papers relevant to the datasetother
: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 newMIAME
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
, andurl
.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; usenotes(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