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)

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)
    }

[Package GenomeGraphs version 1.4.1 Index]