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 1.8.0 Index]