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 ANY`
`chromInfo = ...., # Object of class numeric`
`geneSymbols = ...., # Object of class ANY`
`)`

### 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`:

  An object with an environment-like API 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 or an object with environment-like API 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

      library("hgu95av2.db")

      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)

[Package annotate version 1.65.1 Index]