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)) }