chromLocation-class: 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.

Arguments

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.

Examples

Run this code

  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)