Transcript-class: Represent known transcript isoforms as annoted by Ensembl

In GenomeGraphs: Plotting genomic information from 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))
}

Example output

Loading required package: biomaRt
Loading required package: grid

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