SnpSetIllumina {beadarraySNP}R Documentation

Class to Contain Objects Describing High-Throughput SNP Assays.

Description

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

It supports featureData. Several visualization methods use columns CHR and MapInfo. The CHR column is used to handle sex chromosomes in a specific way. The OPA column is the default way to specify subsamples.

Extends

Directly extends class eSet.

Creating Objects

new('SnpSetIllumina', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], call = [matrix], callProbability = [matrix], G = [matrix], R = [matrix], featureData = [data.frameOrNULL], ...)

SnpSetIllumina instances are usually created through new("SnpSetIllumina", ...). Arguments to new include call (a matrix of gentoypic calls, with features (SNPs) corresponding to rows and samples to columns), callProbability, G, R, phenoData, experimentData, and annotation. phenoData, experimentData, and annotation can be missing, in which case they are assigned default values.

Slots

Inherited from Biobase: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, a matrix callProbability describing the certainty of the call, and matrices R and G to describe allele specific intensities. The contents of these matrices are not enforced by the class. The assayData matrices Gb, Rb, intensity, theta are optional, but are either results or input for several methods of the class. Additional matrices of identical size may also be included in assayData. Class:AssayData
phenoData:
See eSet
experimentData:
See eSet
annotation:
See eSet
featureData:
annotation for SNPs, usually will contain a CHR and a MapInfo column for genomic localization

Methods

Class-specific methods:

exprs(SnpSetIllumina), exprs(SnpSetIllumina,matrix)<-
Access and set elements named call in the AssayData slot.
combine(SnpSetIllumina,SnpSetIllumina):
performs union-like combination in both dimensions of SnpSetIllumina objects
reporterInfo(SnpSetIllumina), reporterInfo(SnpSetIllumina,matrix)<-
Access and set the pData in the featureData slot

Derived from eSet:

sampleNames(SnpSetIllumina) and sampleNames(SnpSetIllumina)<-:
See eSet
featureNames(SnpSetIllumina), featureNames(SnpSetIllumina, value)<-:
See eSet
dims(SnpSetIllumina):
See eSet
phenoData(SnpSetIllumina), phenoData(SnpSetIllumina,value)<-:
See eSet
varLabels(SnpSetIllumina), varLabels(SnpSetIllumina, value)<-:
See eSet
varMetadata(SnpSetIllumina), varMetadata(SnpSetIllumina,value)<-:
See eSet
pData(SnpSetIllumina), pData(SnpSetIllumina,value)<-:
See eSet
varMetadata(SnpSetIllumina), varMetadata(SnpSetIllumina,value)
See eSet
experimentData(SnpSetIllumina),experimentData(SnpSetIllumina,value)<-:
See eSet
pubMedIds(SnpSetIllumina), pubMedIds(SnpSetIllumina,value)
See eSet
abstract(SnpSetIllumina):
See eSet
annotation(SnpSetIllumina), annotation(SnpSetIllumina,value)<-
See eSet
storageMode(eSet), storageMode(eSet,character)<-:
See eSet
reporterNames(SnpSetIllumina), reporterNames(SnpSetIllumina,value)<-:
DEPRECATED
featureData(SnpSetIllumina), featureData(SnpSetIllumina,AnnotatedDataFrame)<-
See eSet
object[(index):
Conducts subsetting of matrices and phenoData and featureData components

Standard generic methods:

initialize(SnpSetIllumina):
Object instantiation, used by new; not to be called directly by the user.
validObject(SnpSetIllumina):
Validity-checking method, ensuring that call, callProbability, G, and R are members of assayData. checkValidity(SnpSetIllumina) imposes this validity check, and the validity checks of Biobase:eSet.
show(SnpSetIllumina)
See eSet
dim(SnpSetIllumina), ncol
See eSet
SnpSetIllumina[(index):
See eSet
SnpSetIllumina$, SnpSetIllumina$<-
See eSet

Author(s)

J. Oosting, based on Biobase eSet class

See Also

eSet


[Package beadarraySNP version 1.0.0 Index]