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.