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

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

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

showClass("gSet")

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.