SnpSet                package:Biobase                R Documentation

Class to Contain Objects Describing High-Throughput SNP Assays.

Description:

     Container for high-throughput assays and experimental metadata.
     'SnpSet' class is derived from 'eSet', and requires matrices
     'call', 'callProbability' as assay data members.

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'

Author(s):

     Martin Morgan, V.J. Carey, after initial design by R. Gentleman

See Also:

     'eSet', 'ExpressionSet'

