Description Objects from the Class Slots Accessors Coercion Author(s) See Also Examples
Virtual Class for Lists of eSets.
A virtual Class: No objects may be created from it.
assayDataList
:Object of class "AssayData"
~~
phenoData
:Object of class "AnnotatedDataFrame"
~~
protocolData
:Object of class "AnnotatedDataFrame"
~~
experimentData
:Object of class "MIAME"
~~
featureDataList
:Object of class "list"
~~
chromosome
:Object of class "vector"
~~
annotation
:Object of class "character"
~~
genome
:Object of class "character"
~~
object
is an instance of a gSetList
-derived class.
annotation(object)
:
character string indicating the package used to provide annotation for the features on the array.
chromosome(object)
:
Returns the chromosome corresponding to each element in the
gSetList
object
elementNROWS(object)
: Returns the number of rows for each
list of assays. In most gSetList
-derived classes, the
assays are organized by chromosome and elementNROWS
returns the number of markers for each chromosome.
genomeBuild(object)
, genomeBuild(object) <- value
:
Get or set the UCSC genome build. Supported builds are hg18 and hg19.
object
is an instance of a gSetList
-derived class.
makeFeatureGRanges(object, ...)
:
Create a GRanges object for the featureData. The featureData is
stored as a list. This method stacks the featureData from each
list element. Metadata columns in the GRanges object include
physical position ('position'), a SNP indicator ('isSnp'), and the
chromosome. The genome build is extracted from object
using
the method genomeBuild
.
R. Scharpf
oligoSetList
, BeadStudioSetList
1 | showClass("gSetList")
|
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