SnpSet
Class to Contain Objects Describing High-Throughput SNP Assays.
Container for high-throughput assays and experimental
metadata. SnpSet
class is derived from
eSet
, and requires matrices call
,
callProbability
as assay data members.
- Keywords
- classes
Extends
Directly extends class eSet
.
Creating Objects
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.
Slots
Inherited from eSet
:
assayData
:- Contains matrices with equal
dimensions, and with column number equal to
nrow(phenoData)
.assayData
must contain a matrixcall
with rows representing features (e.g., SNPs) and columns representing samples, and a matrixcallProbability
describing the certainty of the call. The content ofcall
andcallProbability
are not enforced by the class. Additional matrices of identical size may also be included inassayData
. Class:AssayData-class
phenoData
:- See
eSet
experimentData
:- See
eSet
annotation
:- See
eSet
protocolData
:- See
eSet
Methods
Class-specific methods:
snpCall(SnpSet)
,snpCall(SnpSet,matrix)<-
- Access and
set elements named
call
in theAssayData
slot. exprs(SnpSet)
,exprs(SnpSet,matrix)<-
- Synonym
for
snpCall
. snpCallProbability(SnpSet)
,snpCallProbability<-(SnpSet,matrix)<-
- Access and set
elements named
callProbability
in theAssayData
slot.
eSet
:
updateObject(object, ..., verbose=FALSE)
- Update instance to current version, if necessary. See
updateObject
andeSet
isCurrent(object)
- Determine whether version of object is current. See
isCurrent
isVersioned(object)
- Determine whether object contains a 'version' string describing its structure . See
isVersioned
sampleNames(SnpSet)
andsampleNames(SnpSet)<-
:- See
eSet
featureNames(SnpSet)
,featureNames(SnpSet, value)<-
:- See
eSet
dims(SnpSet)
:- See
eSet
phenoData(SnpSet)
,phenoData(SnpSet,value)<-
:- See
eSet
varLabels(SnpSet)
,varLabels(SnpSet, value)<-
:- See
eSet
varMetadata(SnpSet)
,varMetadata(SnpSet,value)<-
:- See
eSet
pData(SnpSet)
,pData(SnpSet,value)<-
:- See
eSet
varMetadata(SnpSet)
,varMetadata(SnpSet,value)
- See
eSet
experimentData(SnpSet)
,experimentData(SnpSet,value)<-
:- See
eSet
pubMedIds(SnpSet)
,pubMedIds(SnpSet,value)
- See
eSet
abstract(SnpSet)
:- See
eSet
annotation(SnpSet)
,annotation(SnpSet,value)<-
- See
eSet
protocolData(SnpSet)
,protocolData(SnpSet,value)<-
- See
eSet
combine(SnpSet,SnpSet)
:- See
eSet
storageMode(eSet)
,storageMode(eSet,character)<-
:- See
eSet
initialize(SnpSet)
:- Object instantiation, used by
new
; not to be called directly by the user. validObject(SnpSet)
:- Validity-checking method, ensuring that
call
andcallProbability
is a member ofassayData
.checkValidity(SnpSet)
imposes this validity check, and the validity checks ofeSet
. show(SnpSet)
- See
eSet
dim(SnpSet)
,ncol
- See
eSet
SnpSet[(index)
:- See
eSet
SnpSet$
,SnpSet$<-
- See
eSet