chromLocation-class {annotate} | R Documentation |
Class chromLocation, a class for describing genes and their
chromosome mappings.
Description
This class provides chromosomal information provided by a
Bioconductor metadata package. By creating the object once for a
particular package, it can be used in a variety of locations without
the need to recomputed values repeatedly.
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.
See Also
buildChromLocation
Examples
curWarn <- getOption("warn")
options(warn=0)
on.exit(options(warn=curWarn), add=TRUE)
if (require("hgu95av2")) {
z <- buildChromLocation("hgu95av2")
## find the number of chromosomes
nChrom(z)
## Find the names of the chromosomes
chromNames(z)
## get the organism this object refers to
organism(z)
## get the lengths of the chromosomes in this object
chromLengths(z)
} else print("This example requires the hgu95av2 data package")
[Package
annotate version 1.10.0
Index]