SnpSet {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`

[Package Biobase version 2.40.0 Index]