SnpSet {Biobase} | R Documentation |
Container for high-throughput assays and experimental
metadata. SnpSet
class is derived from
eSet
, and requires matrices call
,
callProbability
as assay data members.
Directly extends class eSet
.
new('SnpSet',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
protocolData = [AnnotatedDataFrame],
call = [matrix],
callProbability = [matrix],
...)
SnpSet
instances are usually created through
new("SnpSet", ...)
. Usually the arguments to new
include call
(a matrix of genotypic calls, with features (SNPs)
corresponding to rows and samples to columns), phenoData
,
experimentData
, annotation
, and protocolData
.
phenoData
, experimentData
, annotation
and
protocolData
can be missing, in which case they are assigned
default values.
Inherited from eSet
:
assayData
:nrow(phenoData)
. assayData
must contain a matrix
call
with rows representing features (e.g., SNPs)
and columns representing samples, and a matrix
callProbability
describing the certainty of the
call. The content of call
and callProbability
are
not enforced by the class. Additional matrices of
identical size may also be included in
assayData
. Class:AssayData-class
phenoData
:eSet
experimentData
:eSet
annotation
:eSet
protocolData
:eSet
Class-specific methods:
snpCall(SnpSet)
, snpCall(SnpSet,matrix)<-
call
in the AssayData
slot.
exprs(SnpSet)
, exprs(SnpSet,matrix)<-
snpCall
.
snpCallProbability(SnpSet)
,
snpCallProbability<-(SnpSet,matrix)<-
callProbability
in the AssayData
slot.
Derived from eSet
:
updateObject(object, ..., verbose=FALSE)
updateObject
and eSet
isCurrent(object)
isCurrent
isVersioned(object)
isVersioned
sampleNames(SnpSet)
and sampleNames(SnpSet)<-
:eSet
featureNames(SnpSet)
, featureNames(SnpSet, value)<-
:eSet
dims(SnpSet)
:eSet
phenoData(SnpSet)
, phenoData(SnpSet,value)<-
:eSet
varLabels(SnpSet)
, varLabels(SnpSet, value)<-
:eSet
varMetadata(SnpSet)
, varMetadata(SnpSet,value)<-
:eSet
pData(SnpSet)
, pData(SnpSet,value)<-
:eSet
varMetadata(SnpSet)
, varMetadata(SnpSet,value)
eSet
experimentData(SnpSet)
,experimentData(SnpSet,value)<-
:eSet
pubMedIds(SnpSet)
, pubMedIds(SnpSet,value)
eSet
abstract(SnpSet)
:eSet
annotation(SnpSet)
, annotation(SnpSet,value)<-
eSet
protocolData(SnpSet)
, protocolData(SnpSet,value)<-
eSet
combine(SnpSet,SnpSet)
:eSet
storageMode(eSet)
, storageMode(eSet,character)<-
:eSet
Standard generic methods:
initialize(SnpSet)
:new
; not to be called directly by the user.validObject(SnpSet)
:call
and callProbability
is a member of assayData
. checkValidity(SnpSet)
imposes this validity check, and the validity checks of eSet
.show(SnpSet)
eSet
dim(SnpSet)
, ncol
eSet
SnpSet[(index)
:eSet
SnpSet$
, SnpSet$<-
eSet
Martin Morgan, V.J. Carey, after initial design by R. Gentleman