SnpSet2-class {oligoClasses} | R Documentation

## Class `"SnpSet2"`

### Description

A container for genotype calls and confidence scores. Similar to the `SnpSet` class in Biobase, but `SnpSet2` extends `gSet` directly whereas `SnpSet` extends `eSet`. Useful properties of `gSet` include the `genome` slot and the `GenomeAnnotatedDataFrame`.

### Objects from the Class

Objects can be created by calls of the form `new("SnpSet2", assayData, phenoData, featureData, experimentData, annotation, protocolData, call, callProbability, genome, ...)`.

### Slots

`genome`:

  Object of class `"character"` indicating the UCSC genome build. Supported builds are 'hg18' and 'hg19'.

`assayData`:

  Object of class `"AssayData"`.

`phenoData`:

  Object of class `"AnnotatedDataFrame"`.

`featureData`:

  Object of class `"AnnotatedDataFrame"`.

`experimentData`:

  Object of class `"MIAxE"`.

`annotation`:

  Object of class `"character"` ~~

`protocolData`:

  Object of class `"AnnotatedDataFrame"` ~~

`.__classVersion__`:

  Object of class `"Versions"` ~~

### Extends

Class `"gSet"`, directly. Class `"eSet"`, by class "gSet", distance 2. Class `"VersionedBiobase"`, by class "gSet", distance 3. Class `"Versioned"`, by class "gSet", distance 4.

### Accessors

The argument `object` for the following methods is an instance of the `SnpSet2` class.

  `calls(object)`: `calls(object) <- value`:

  Gets or sets the genotype calls. `value` can be a `matrix` or a `ff_matrix`.

  `confs(object)`: `confs(object) <- value`:

  Gets or sets the genotype confidence scores. `value` can be a `matrix` or a `ff_matrix`.

  `snpCall(object)`: `snpCallProbability(object) <- value`:

  Gets or sets the genotype confidence scores.

### Author(s)

R. Scharpf

### See Also

`SnpSet`

### Examples

    showClass("SnpSet2")
    new("SnpSet2")

[Package oligoClasses version 1.48.0 Index]