Gene-class {GenomeGraphs} | R Documentation |
Class "Gene" represents the Ensembl Gene level annotation. Upon creation of an object of this class, intron and exon boundaries are retrieved from Ensembl
Objects can be created by calls of the form new("Gene", ...)
.
id
:"character"
, representing a unique identifier for the gene or a vector of identifiers for genes that are located near each other (or at least on the same chromosome)type
:"character"
, representing the type of identifier used, e.g. hgnc_symbol, entrezgene and ensembl_gene_id, check the listFilters function of the biomaRt package for more identifier optionssize
:"numeric"
, specifies the size of the plotcolor
:"character"
, specifies the color of the exons biomart
:"Mart"
, contains the link to the Ensembl database and should be created using the useMart function from the biomaRt package ens
:"data.frame"
, contains the output from the Ensembl query, users don't need to give a value to this signature(.Object = "Gene")
: ... signature(.Object = "Gene")
: ... signature(object = "Gene")
: ... Jim Bullard and Steffen Durinck
http://www.stat.berkeley.edu/~steffen/
objects to See Also as gdPlot
if(interactive()){ mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") gene = new("Gene", id = "ENSG00000095203", type="ensembl_gene_id", biomart = mart) gdPlot(list(gene), minBase= 110974000, maxBase = 111122900) }