Transcript-class {GenomeGraphs} | R Documentation

## Represent known transcript isoforms as annoted by Ensembl

### Description

Represent known transcript isoforms as annoted by Ensembl

### Objects from the Class

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

### Slots

`id`:

  Object of class `"character"`, represents the gene identifier that should be used to retrieve the tanscript level annotation

`type`:

  Object of class `"character"`, represents the type of identifiers used to specify the gene e.g. hgnc\_symbol, entrezgene and ensembl\_gene\_id

`transcriptSize`:

  Object of class `"numeric"`, represents the size of the transcripts in the plot

`numOfTranscripts`:

  Object of class `"numeric"`, should not be used bu users

`biomart`:

  Object of class `"Mart"`, containing the links to the Ensembl database. This object should be created with the useMart function of the biomaRt package

`ens`:

  Object of class `"data.frame"`, should not be used by the users. Contains the output from the biomaRt query

### Methods

drawGD

  `signature(.Object = "Transcript")`: ...

initialize

  `signature(.Object = "Transcript")`: ...

show

  `signature(object = "Transcript")`: ...

### Author(s)

Steffen Durinck

### References

http://www.stat.berkeley.edu/~steffen/

### See Also

objects to See Also as `gdPlot`

### Examples

    if(interactive()){
    data("unrData", package="GenomeGraphs")
    mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
    transcript = new("Transcript", id ="ENSG00000009307" , biomart = mart)
    gdPlot(list(transcript), minBase = min(exon@probeStart), maxBase=max(exon@probeEnd))
    }

[Package GenomeGraphs version 1.42.0 Index]