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
:"numeric"
, start positionend
:"numeric"
, end position chromosome
:"character"
, chromosome name strand
:"character"
, represents the strand from which the gene structures should be retrieved. Value is either + or -size
:"numeric"
, represents the size of the GeneRegion in the final plot color
:"character"
, represents the color to be used to plot the exons biomart
:"Mart"
, containing the link to the Ensembl database. This should be created by the useMart function from the biomaRt packageens
:"data.frame"
, output of the biomaRt query, should not be used by userssignature(.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) }