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 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:- 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 the AssayData
slot. exprs(SnpSet), exprs(SnpSet,matrix)<-- Synonym
for
snpCall. snpCallProbability(SnpSet),
snpCallProbability<-(SnpSet,matrix)<-- Access and set
elements named
callProbability in the AssayData
slot.
Derived from eSet:
updateObject(object, ..., verbose=FALSE)- Update instance to current version, if necessary. See
updateObject and eSet 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) and sampleNames(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
Standard generic methods:
initialize(SnpSet):- Object instantiation, used by
new; not to be called directly by the user. validObject(SnpSet):- Validity-checking method, ensuring that
call and callProbability is a member of assayData. checkValidity(SnpSet) imposes this validity check, and the validity checks of eSet. show(SnpSet)- See
eSet dim(SnpSet), ncol- See
eSet SnpSet[(index):- See
eSet SnpSet$, SnpSet$<-- See
eSet