Gene-class {GenomeGraphs}R Documentation

Class "Gene" represents the Ensembl Gene level annotation

Description

Class "Gene" represents the Ensembl Gene level annotation. Upon creation of an object of this class, intron and exon boundaries are retrieved from Ensembl

Objects from the Class

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

Slots

id:
Object of class "character", representing a unique identifier for the gene or a vector of identifiers for genes that are located near each other (or at least on the same chromosome)
type:
Object of class "character", representing the type of identifier used, e.g. hgnc_symbol, entrezgene and ensembl_gene_id, check the listFilters function of the biomaRt package for more identifier options
size:
Object of class "numeric", specifies the size of the plot
color:
Object of class "character", specifies the color of the exons
biomart:
Object of class "Mart", contains the link to the Ensembl database and should be created using the useMart function from the biomaRt package
ens:
Object of class "data.frame", contains the output from the Ensembl query, users don't need to give a value to this

Methods

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

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")
gene = new("Gene", id = "ENSG00000095203", type="ensembl_gene_id", biomart = mart)
gdPlot(list(gene), minBase= 110974000, maxBase = 111122900)
}

[Package GenomeGraphs version 1.0.1 Index]