SnpSetIllumina {beadarraySNP} | R Documentation |
Container for high-throughput assays and experimental metadata.
SnpSetIllumina
class is derived from
eSet
, and requires matrices
R
, G
, call
, callProbability
as assay data members.
It supports featureData. Several visualization methods use columns CHR
and MapInfo
. The CHR
column is used to handle sex chromosomes in
a specific way. The OPA
column is the default way to specify subsamples.
Directly extends class eSet
.
new('SnpSetIllumina',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
call = [matrix],
callProbability = [matrix],
G = [matrix],
R = [matrix],
featureData = [data.frameOrNULL],
...)
SnpSetIllumina
instances are usually created through
new("SnpSetIllumina", ...)
. Arguments to new
include call
(a matrix of gentoypic calls, with features (SNPs)
corresponding to rows and samples to columns), callProbability
,
G
, R
, phenoData
, experimentData
, and annotation
.
phenoData
, experimentData
, and annotation
can be
missing, in which case they are assigned default values.
Inherited from Biobase:eSet
:
assayData
:nrow(phenoData)
. assayData
must
contain a matrix call
with rows representing features (e.g., SNPs)
and columns representing samples, a matrix callProbability
describing the certainty of the call, and matrices R
and G
to describe allele specific intensities. The contents of these matrices
are not enforced by the class. The assayData
matrices Gb, Rb,
intensity, theta
are optional, but are either results or input for
several methods of the class. Additional matrices of identical size may
also be included in assayData
. Class:AssayData
.phenoData
:eSet
.experimentData
:eSet
.annotation
:eSet
.featureData
:CHR
and a MapInfo
column for genomic localization.Class-specific methods:
exprs(SnpSetIllumina)
, exprs(SnpSetIllumina,matrix)<-
call
in the AssayData
slot.combine(SnpSetIllumina,SnpSetIllumina)
:union
-like
combination in both dimensions of SnpSetIllumina objects.fData(SnpSetIllumina)
, fData(SnpSetIllumina,data.frame)<-
pData
in the featureData slot.calculateGSR(SnpSetIllumina)
assayData
. Should be performed before combining datasets.
Derived from eSet
:
sampleNames(SnpSetIllumina)
and sampleNames(SnpSetIllumina)<-
:eSet
.featureNames(SnpSetIllumina)
, featureNames(SnpSetIllumina, value)<-
:eSet
.dims(SnpSetIllumina)
:eSet
.phenoData(SnpSetIllumina)
, phenoData(SnpSetIllumina,value)<-
:eSet
.varLabels(SnpSetIllumina)
, varLabels(SnpSetIllumina, value)<-
:eSet
.varMetadata(SnpSetIllumina)
, varMetadata(SnpSetIllumina,value)<-
:eSet
.pData(SnpSetIllumina)
, pData(SnpSetIllumina,value)<-
:eSet
.varMetadata(SnpSetIllumina)
, varMetadata(SnpSetIllumina,value)
eSet
.experimentData(SnpSetIllumina)
,experimentData(SnpSetIllumina,value)<-
:eSet
.pubMedIds(SnpSetIllumina)
, pubMedIds(SnpSetIllumina,value)
eSet
.abstract(SnpSetIllumina)
:eSet
.annotation(SnpSetIllumina)
, annotation(SnpSetIllumina,value)<-
eSet
.storageMode(eSet)
, storageMode(eSet,character)<-
:eSet
.featureData(SnpSetIllumina)
, featureData(SnpSetIllumina,AnnotatedDataFrame)<-
eSet
.object[(index)
:Standard generic methods:
initialize(SnpSetIllumina)
:new
; not to be called directly by the user.validObject(SnpSetIllumina)
:call
, callProbability
, G
, and R
are members of
assayData
. checkValidity(SnpSetIllumina)
imposes this
validity check, and the validity checks of Biobase:eSet
.show(SnpSetIllumina)
eSet
.dim(SnpSetIllumina)
, ncol
eSet
.SnpSetIllumina[(index)
:eSet
.SnpSetIllumina$
, SnpSetIllumina$<-
eSet
.J. Oosting, based on Biobase eSet class