GeneRegion-class {GenomeGraphs}R Documentation

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

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 -
size:
Object of class "numeric", represents the size of the GeneRegion in the final plot
color:
Object of class "character", represents the color to be used to plot the exons
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

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)
}

[Package GenomeGraphs version 1.2.3 Index]