chromLocation-class | R Documentation |
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.
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
)
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
(chromLocation): Gets the lengths of the chromosome for this organism
(chromLocation): Gets the 'chromLocs' attribute.
(chromLocation): Gets the name of the chromosomes for this organism
(chromLocation): Gets the 'dataSource' attribute.
(chromLocation): Gets the 'probesToChrom' attribute.
(chromLocation): gets the number of chromosomes this organism has
(chromLocation): gets the 'organism' attribute.
Gets the 'chromInfo' attribute.
Gets the 'geneSymbols' attribute.
buildChromLocation
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)
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