Class "AlleleSet"

Description

A class for storing the locus-level summaries of the normalized intensities

Objects from the Class

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

Slots

assayData:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

featureData:

Object of class "AnnotatedDataFrame" ~~

experimentData:

Object of class "MIAME" ~~

annotation:

Object of class "character" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

.__classVersion__:

Object of class "Versions" ~~

Extends

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

Methods

allele

signature(object = "AlleleSet"): extract allele specific summaries. For 50K (XBA and Hind) and 250K (Sty and Nsp) arrays, an additional argument (strand) must be used (allowed values: 'sense', 'antisense'.

bothStrands

signature(object = "AlleleSet"): tests if data contains allele summaries on both strands for a given SNP.

bothStrands

signature(object = "SnpFeatureSet"): tests if data contains allele summaries on both strands for a given SnpFeatureSet.

db

signature(object = "AlleleSet"): link to database connection.

getA

signature(object = "AlleleSet"): average intensities (across alleles)

getM

signature(object = "AlleleSet"): log-ratio (Allele A vs. Allele B)

Author(s)

R. Scharpf

See Also

SnpSuperSet, CNSet

Examples

showClass("AlleleSet")
## an empty AlleleSet
x <- new("matrix")
new("AlleleSet", senseAlleleA=x, senseAlleleB=x, antisenseAlleleA=x, antisenseAlleleB=x)
##or
new("AlleleSet", alleleA=x, alleleB=x)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(oligoClasses)
Welcome to oligoClasses version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligoClasses/AlleleSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AlleleSet-class
> ### Title: Class "AlleleSet"
> ### Aliases: AlleleSet-class AlleleSet allele allele,AlleleSet-method
> ###   allele,SnpFeatureSet-method bothStrands bothStrands,AlleleSet-method
> ###   bothStrands,SnpFeatureSet-method db,AlleleSet-method
> ###   getA,AlleleSet-method getM,AlleleSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("AlleleSet")
Class "AlleleSet" [package "oligoClasses"]

Slots:
                                                               
Name:           assayData          phenoData        featureData
Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
                                                               
Name:      experimentData         annotation       protocolData
Class:              MIAxE          character AnnotatedDataFrame
                         
Name:   .__classVersion__
Class:           Versions

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

Known Subclasses: "SnpSuperSet"
> ## an empty AlleleSet
> x <- new("matrix")
> new("AlleleSet", senseAlleleA=x, senseAlleleB=x, antisenseAlleleA=x, antisenseAlleleB=x)
AlleleSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples 
  element names: antisenseAlleleA, antisenseAlleleB, senseAlleleA, senseAlleleB 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
> ##or
> new("AlleleSet", alleleA=x, alleleB=x)
AlleleSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples 
  element names: alleleA, alleleB 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>