AnnotatedSnpCallSet-class {SNPchip}R Documentation

Class "AnnotatedSnpCallSet"

Description

Container for genotype call data accompanied by SNP annotation

Objects from the Class

Objects can be created by calls of the form new("AnnotatedSnpCallSet", phenoData, experimentData, annotation, calls, callsConfidence, snpLocation, chromosomeAnnotation, chromosome).

Slots

chromosomeAnnotation:
Object of class data.frame
assayData:
Object of class AssayData
phenoData:
Object of class AnnotatedDataFrame
featureData:
Object of class AnnotatedDataFrame contains annotation for the SNP's, such as chromosome, physical position, and alleles.
experimentData:
Object of class MIAME
annotation:
For 100k chips, "mapping50kHind240", "mapping50kXba240" , or "mapping100k". For 500k chips, mmust be "mapping250kNsp" or "mapping250kSty"
.__classVersion__:
Object of class Versions

Extends

Class SnpCallSet, directly. Class eSet, by class SnpCallSet. Class VersionedBiobase, by class SnpCallSet. Class Versioned, by class SnpCallSet.

Methods

Note

Author(s)

Robert Scharpf

See Also

Examples






[Package SNPchip version 1.0.0 Index]