gSet-class {oligoClasses} | R Documentation

## Container for objects with genomic annotation on SNPs

### Description

Container for objects with genomic annotation on SNPs

### Objects from the Class

A virtual Class: No objects may be created from it.

### Slots

`featureData`:

  Object of class `"GenomeAnnotatedDataFrame"` ~~

`assayData`:

  Object of class `"AssayData"` ~~

`phenoData`:

  Object of class `"AnnotatedDataFrame"` ~~

`experimentData`:

  Object of class `"MIAxE"` ~~

`annotation`:

  Object of class `"character"` ~~

`protocolData`:

  Object of class `"AnnotatedDataFrame"` ~~

`genome`:

  Object of class `"character"` ~~

`.__classVersion__`:

  Object of class `"Versions"` ~~

### Extends

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

### Methods

The `object` for the below methods is a class that extends the virtual class `gSet`.

  `checkOrder(object)`: checks that the object is ordered by chromosome and physical position. Returns `logical`.

  `chromosome(object)`: accessor for chromosome in the `GenomeAnnotatedDataFrame` slot.

  `chromosome(object) <- value`: replacement method for chromosome in the `GenomeAnnotatedDataFrame` slot. `value` must be an `integer` vector.

  `db(object)`: database connection

  `genomeBuild(object)`, `genomeBuild(object) <- value`:

  Get or set the UCSC genome build. Supported builds are hg18 and hg19.

  `getArm(object)`: Character vector indicating the chromosomal arm for each marker in `object`.

  `isSnp(object)`: whether the marker is polymorphic. Returns a `logical` vector.

  `makeFeatureGRanges(object)`: Construct an instance of the `GRanges` class from a `GenomeAnnotatedDataFrame`.

  `position(object)`: `integer` vector of the genomic position

  `show(object)`:

  Print a concise summary of `object`.

### Author(s)

R. Scharpf

### See Also

`chromosome`, `position`, `isSnp`

### Examples

    showClass("gSet")

[Package oligoClasses version 1.50.4 Index]