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
size:
Object of class "numeric", represents the size of the plot of this object
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
color:
Object of class "character", color of the exons
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 1.0.1 Index]