| Transcript-class {GenomeGraphs} | R Documentation |
Represent known transcript isoforms as annoted by Ensembl
Objects can be created by calls of the form new("Transcript", ...).
id:"character", represents the gene identifier that should be used to retrieve the tanscript level annotation type:"character", represents the type of identifiers used to specify the gene e.g. hgnc_symbol, entrezgene and ensembl_gene_idsize:"numeric", represents the size of the plot of this objecttranscriptSize:"numeric", represents the size of the transcripts in the plotnumOfTranscripts:"numeric", should not be used bu users color:"character", color of the exonsbiomart:"Mart", containing the links to the Ensembl database. This object should be created with the useMart function of the biomaRt package ens:"data.frame", should not be used by the users. Contains the output from the biomaRt query signature(.Object = "Transcript"): ... signature(.Object = "Transcript"): ... signature(object = "Transcript"): ... Steffen Durinck
http://www.stat.berkeley.edu/~steffen/
objects to See Also as gdPlot
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))
}