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 matricies `call`, `callProbability` as assay data members.

### Extends

Directly extends class `eSet`.

### Creating Objects

`new('SnpSet', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], call = [matrix], callProbability = [matrix], ...)`

`SnpSet` instances are usually created through `new("SnpSet", ...)`. Usually the arguments to `new` include `call` (a matrix of gentoypic calls, with features (SNPs) corresponding to rows and samples to columns), `phenoData`, `experimentData`, and `annotation`. `phenoData`, `experimentData`, and `annotation` 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 represening 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`

### Methods

Class-specific methods:

`exprs(SnpSet)`, `exprs(SnpSet,matrix)<-`
  Access and set elements named `call` 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`
`combine(SnpSet,SnpSet)`:
  See `eSet`
`storageMode(eSet)`, `storageMode(eSet,character)<-`:
  See `eSet`
`reporterNames(SnpSet)`, `reporterNames(SnpSet,value)<-`:
  DEPRECATED

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)

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

### See Also

`eSet`, `ExpressionSet`

[Package Biobase version 1.14.1 Index]