AlleleSet-class {oligoClasses} | R Documentation |
A class for storing the locus-level summaries of the normalized intensities
Objects can be created by calls of the form new("AlleleSet", assayData, phenoData, featureData, experimentData, annotation, protocolData, ...)
.
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"
~~
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
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'.
signature(object = "AlleleSet")
: tests if
data contains allele summaries on both strands for a given SNP.
signature(object = "SnpFeatureSet")
: tests if
data contains allele summaries on both strands for a given SnpFeatureSet.
signature(object = "AlleleSet")
: link to database connection.
signature(object = "AlleleSet")
: average
intensities (across alleles)
signature(object = "AlleleSet")
: log-ratio
(Allele A vs. Allele B)
R. Scharpf
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)