chromLocation-class {annotate}R Documentation

Class chromLocation, a class for describing genes and their chromosome mappings.

Description

This class provides a mechanism for mapping a set of genes to their respective locations in chromosomes. Details on how to construct an object of this class from Bioconductor data packags are given in the byChroms vignette in the geneplotter package.

Creating Objects

new('chromLocation',
organism = ...., # Object of class character
dataSource = ...., # Object of class character
chromLocs = ...., # Object of class list
probesToChrom = ...., # Object of class environment
chromInfo = ...., # Object of class numeric
geneSymbols = ...., # Object of class environment
)

Slots

organism:
Object of class "character". The organism that these genes correspond to.
dataSource:
Object of class "character". The source of the gene data.
chromLocs:
Object of class "list". A list which provides specific location information for every gene.
probesToChrom:
Object of class "genEnv". A hash table which will translate a probe identifier to chromosome it belongs to.
chromInfo:
A numerical vector representing each chromosome, where the names are the names of the chromosomes and the values are their lengths
geneSymbols:
An environment that maps a probe ID to the appropriate gene symbol

Methods

chromLengths
(chromLocation): Gets the lengths of the chromosome for this organism
chromLocs
(chromLocation): Gets the 'chromLocs' attribute.
chromNames
(chromLocation): Gets the name of the chromosomes for this organism
dataSource
(chromLocation): Gets the 'dataSource' attribute.
probesToChrom
(chromLocation): Gets the 'probesToChrom' attribute.
nChrom
(chromLocation): gets the number of chromosomes this organism has
organism
(chromLocation): gets the 'organism' attribute.
chromInfo
Gets the 'chromInfo' attribute.
geneSymbols
Gets the 'geneSymbols' attribute.

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