chromosome-methods {oligoClasses} | R Documentation

## Methods for function chromosome in package oligoClasses

### Description

Methods for function `chromosome` in package oligoClasses ~~

### Methods

The methods for `chromosome` extracts the chromosome (represented as an integer) for each marker in a `eSet`-derived class or a `AnnotatedDataFrame`-derived class.

`signature(object = "AnnotatedDataFrame")`

  Accessor for chromosome.

`signature(object = "eSet")`

  If 'chromosome' is included in `fvarLabels(object)`, the integer representation of the chromosome will be returned. Otherwise, an error is thrown.

`signature(object = "GenomeAnnotatedDataFrame")`

  Accessor for chromosome. If annotation was not available due to a missing or non-existent annotation package, the value returned by the accessor will be a vector of zero's.

  `(chromosome(object) <- value)`: Assign chromosome to the `AnnotatedDataFrame` slot of an `eSet`-derived `object`.

`signature(object = "RangedDataCNV")`

  Accessor for chromosome.

### Note

Integer representation: chr X = 23, chr Y = 24, chr XY = 25. Symbols M, Mt, and MT are coded as 26.

### See Also

`chromosome2integer`

### Examples

    chromosome2integer(c(1:22, "X", "Y", "XY", "M"))

[Package oligoClasses version 1.46.0 Index]