GeneRegion-class: Class "GeneRegion", representing gene structures in a defined...
In GenomeGraphs: Plotting genomic information from Ensembl

Description Objects from the Class Slots Methods Author(s) References See Also Examples

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

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

drawGD: signature(.Object = "GeneRegion"): ...
initialize: signature(.Object = "GeneRegion"): ...
show: signature(object = "GeneRegion"): ...

Steffen Durinck

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

objects to See Also as gdPlot

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)
}