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 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

See Also

eSet, ExpressionSet

Aliases
  • class:SnpSet
  • SnpSet
  • SnpSet-class
  • exprs<-,SnpSet,matrix-method
  • exprs,SnpSet-method
  • snpCall,SnpSet-method
  • snpCall<-,SnpSet,matrix-method
  • snpCallProbability,SnpSet-method
  • snpCallProbability<-,SnpSet,matrix-method
  • initialize,SnpSet-method
Documentation reproduced from package Biobase, version 2.26.0, License: Artistic-2.0

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