gSet-class: Container for objects with genomic annotation on SNPs

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

Description

Container for objects with genomic annotation on SNPs

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

featureData:

Object of class "GenomeAnnotatedDataFrame" ~~

assayData:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

experimentData:

Object of class "MIAxE" ~~

annotation:

Object of class "character" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

genome:

Object of class "character" ~~

.__classVersion__:

Object of class "Versions" ~~

Extends

Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.

Methods

The object for the below methods is a class that extends the virtual class gSet.

checkOrder(object): checks that the object is ordered by chromosome and physical position. Returns logical.

chromosome(object): accessor for chromosome in the GenomeAnnotatedDataFrame slot.

chromosome(object) <- value: replacement method for chromosome in the GenomeAnnotatedDataFrame slot. value must be an integer vector.

db(object): database connection

genomeBuild(object), genomeBuild(object) <- value:

Get or set the UCSC genome build. Supported builds are hg18 and hg19.

getArm(object): Character vector indicating the chromosomal arm for each marker in object.

isSnp(object): whether the marker is polymorphic. Returns a logical vector.

makeFeatureGRanges(object): Construct an instance of the GRanges class from a GenomeAnnotatedDataFrame.

position(object): integer vector of the genomic position

show(object):

Print a concise summary of object.

Author(s)

R. Scharpf

See Also

chromosome, position, isSnp

Examples

1
showClass("gSet")

benilton/oligoClasses-release documentation built on May 11, 2017, 4:19 a.m.