SnpSet2-class: Class '"SnpSet2"'

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

Description

A container for genotype calls and confidence scores. Similar to the SnpSet class in Biobase, but SnpSet2 extends gSet directly whereas SnpSet extends eSet. Useful properties of gSet include the genome slot and the GenomeAnnotatedDataFrame.

Objects from the Class

Objects can be created by calls of the form new("SnpSet2", assayData, phenoData, featureData, experimentData, annotation, protocolData, call, callProbability, genome, ...).

Slots

genome:

Object of class "character" indicating the UCSC genome build. Supported builds are 'hg18' and 'hg19'.

assayData:

Object of class "AssayData".

phenoData:

Object of class "AnnotatedDataFrame".

featureData:

Object of class "AnnotatedDataFrame".

experimentData:

Object of class "MIAxE".

annotation:

Object of class "character" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

.__classVersion__:

Object of class "Versions" ~~

Extends

Class "gSet", directly. Class "eSet", by class "gSet", distance 2. Class "VersionedBiobase", by class "gSet", distance 3. Class "Versioned", by class "gSet", distance 4.

Accessors

The argument object for the following methods is an instance of the SnpSet2 class.

calls(object): calls(object) <- value:

Gets or sets the genotype calls. value can be a matrix or a ff_matrix.

confs(object): confs(object) <- value:

Gets or sets the genotype confidence scores. value can be a matrix or a ff_matrix.

snpCall(object): snpCallProbability(object) <- value:

Gets or sets the genotype confidence scores.

Author(s)

R. Scharpf

See Also

SnpSet

Examples

showClass("SnpSet2")
new("SnpSet2")

oligoClasses documentation built on Nov. 8, 2020, 5:32 p.m.