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]