GeneRegion-class {GenomeGraphs} | R Documentation |
Given a start and end position and a chromosome name, all gene structures in this region will be retrieved from Ensembl upon creation of the object.
Objects can be created by calls of the form new("GeneRegion", ...)
.
start
:Object of class "numeric"
, start position
end
:Object of class "numeric"
, end position
chromosome
:Object of class "character"
, chromosome name
strand
:Object of class "character"
, represents the strand from which the gene structures should be retrieved. Value is either + or -
biomart
:Object of class "Mart"
, containing the link to the Ensembl database. This should be created by the useMart function from the biomaRt package
ens
:Object of class "data.frame"
, output of the biomaRt query, should not be used by users
signature(.Object = "GeneRegion")
: ...
signature(.Object = "GeneRegion")
: ...
signature(object = "GeneRegion")
: ...
Steffen Durinck
http://www.stat.berkeley.edu/~steffen/
objects to See Also as gdPlot
if(interactive()){ mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end = 30550000, strand = "+", biomart = mart) genomeAxis = new("GenomeAxis", add53=TRUE) gdPlot(list(genomeAxis, plusStrand), minBase = 30450000, maxBase = 30550000) }