Class "GeneRegion", representing gene structures in a defined genomic region

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Description

Given a start and end position and a chromosome name, all gene structures in this region will be retrieved from Ensembl upon creation of the object.

Objects from the Class

Objects can be created by calls of the form new("GeneRegion", ...).

Slots

start:

Object of class "numeric", start position

end:

Object of class "numeric", end position

chromosome:

Object of class "character", chromosome name

strand:

Object of class "character", represents the strand from which the gene structures should be retrieved. Value is either + or -

biomart:

Object of class "Mart", containing the link to the Ensembl database. This should be created by the useMart function from the biomaRt package

ens:

Object of class "data.frame", output of the biomaRt query, should not be used by users

Methods

drawGD

signature(.Object = "GeneRegion"): ...

initialize

signature(.Object = "GeneRegion"): ...

show

signature(object = "GeneRegion"): ...

Author(s)

Steffen Durinck

References

http://www.stat.berkeley.edu/~steffen/

See Also

objects to See Also as gdPlot

Examples

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if(interactive()){
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end = 30550000, strand = "+", biomart = mart)
genomeAxis = new("GenomeAxis", add53=TRUE)
gdPlot(list(genomeAxis, plusStrand), minBase = 30450000, maxBase =  30550000)
}

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