chromosome-methods: Methods for function chromosome in package oligoClasses

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

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"))

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.