Gene-class: Class "Gene" represents the Ensembl Gene level annotation

In GenomeGraphs: Plotting genomic information from Ensembl

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

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)

Jim Bullard and 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)
}

Example output

Loading required package: biomaRt
Loading required package: grid

GenomeGraphs documentation built on Oct. 31, 2019, 4:34 a.m.