SnpLevelSet-class {oligoClasses}R Documentation

Class "SnpLevelSet"

Description

Virtual class for SNP-level data

Objects from the Class

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

Slots

assayData:
The usual restrictions on assayData: contains matrices with equal dimensions, and with column number equal to nrow(phenoData). Class:class.AssayData
phenoData:
See class.eSet
featureData:
See class.eSet
experimentData:
See class.eSet
annotation:
See class.eSet
.__classVersion__:
Object of class "Versions"

Extends

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

Methods

calls
signature(object = "SnpLevelSet"): Accessor for matrix of genotype calls
calls<-
signature(object = "SnpLevelSet", value = "matrix"): Replacement method for genotype calls.
callsConfidence
signature(object = "SnpLevelSet"): Accessor for matrix of confidence scores for the genotype calls
callsConfidence<-
signature(object = "SnpLevelSet", value = "matrix"): Replacement method
chromosome
signature(object = "SnpLevelSet"): See also chromosome
chromosome<-
signature(object = "SnpLevelSet", value = "character"): See also chromosome
cnConfidence
signature(object = "SnpLevelSet"): Accessor for matrix of confidence scores for the copy number estimates.
cnConfidence<-
signature(object = "SnpLevelSet", value = "matrix"): Replacement method for confidence scores of copy number estimates.
combine
signature(x = "SnpLevelSet", y = "SnpLevelSet"): Useful for combining two objects with the same phenoData. For instance, combine an object created from the Hind 50k chip and an object created from the Xba 50k chip.
copyNumber
signature(object = "SnpLevelSet"): Accessor for matrix of copy numbers.
copyNumber<-
signature(object = "SnpLevelSet", value = "matrix"): Replacement method for copy number matrices
db
signature(object = "SnpLevelSet"): See also db
position
signature(object = "SnpLevelSet"): See also position

Author(s)

RS

Examples

showClass("SnpLevelSet")

[Package oligoClasses version 1.4.0 Index]