AlleleSet-class: Class "AlleleSet"

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

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)

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