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 1.12.1 Index]